Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

Energy Technology Data Exchange (ETDEWEB)

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

2012-06-15

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

Characterization of Olkiluoto bacterial and archaeal communities by 454 pyrosequencing

International Nuclear Information System (INIS)

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

2012-06-01

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

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

Science.gov (United States)

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

2009-01-01

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

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing.

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Galitskaya, Polina; Biktasheva, Liliya; Saveliev, Anatoly; Grigoryeva, Tatiana; Boulygina, Eugenia; Selivanovskaya, Svetlana

2017-01-01

Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 106 and (0.4±0.0) x 107 g-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x105 and (6.1±0.2) x105 ITS copies g-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing.

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Polina Galitskaya

Full Text Available Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil and one discriminate component (sewage sludges of different origin were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2 x 106 and (0.4±0.0 x 107 g-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0 x105 and (6.1±0.2 x105 ITS copies g-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

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Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

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

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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.

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

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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.

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

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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...

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

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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.

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

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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.

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.

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

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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.

Rapid Molecular Identification of Human Taeniid Cestodes by Pyrosequencing Approach

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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

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

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Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

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.

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

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.

Rapid molecular identification of human taeniid cestodes by pyrosequencing approach.

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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.

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

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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...

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

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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.

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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.

Managing mechanistic and organic structure in health care organizations.

Science.gov (United States)

Olden, Peter C

2012-01-01

Managers at all levels in a health care organization must organize work to achieve the organization's mission and goals. This requires managers to decide the organization structure, which involves dividing the work among jobs and departments and then coordinating them all toward the common purpose. Organization structure, which is reflected in an organization chart, may range on a continuum from very mechanistic to very organic. Managers must decide how mechanistic versus how organic to make the entire organization and each of its departments. To do this, managers should carefully consider 5 factors for the organization and for each individual department: external environment, goals, work production, size, and culture. Some factors may push toward more mechanistic structure, whereas others may push in the opposite direction toward more organic structure. Practical advice can help managers at all levels design appropriate structure for their departments and organization.

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...

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

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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

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

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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.

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.

Deep 16S rRNA Pyrosequencing Reveals a Bacterial Community Associated with Banana Fusarium Wilt Disease Suppression Induced by Bio-Organic Fertilizer Application

Science.gov (United States)

Ruan, Yunze; Xue, Chao; Zhang, Jian; Li, Rong; Shen, Qirong

2014-01-01

Our previous work demonstrated that application of a bio-organic fertilizer (BIO) to a banana mono-culture orchard with serious Fusarium wilt disease effectively decreased the number of soil Fusarium sp. and controlled the soil-borne disease. Because bacteria are an abundant and diverse group of soil organisms that responds to soil health, deep 16 S rRNA pyrosequencing was employed to characterize the composition of the bacterial community to investigate how it responded to BIO or the application of other common composts and to explore the potential correlation between bacterial community, BIO application and Fusarium wilt disease suppression. After basal quality control, 137,646 sequences and 9,388 operational taxonomic units (OTUs) were obtained from the 15 soil samples. Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria were the most frequent phyla and comprised up to 75.3% of the total sequences. Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance. Meanwhile, on genus level, higher abundances compared to other treatments were observed for Gemmatimonas and Gp4. Correlation and redundancy analysis showed that the abundance of Gemmatimonas and Sphingomonas and the soil total nitrogen and ammonium nitrogen content were higher after BIO application, and they were all positively correlated with disease suppression. Cumulatively, the reduced Fusarium wilt disease incidence that was seen after BIO was applied for 1-year might be attributed to the general suppression based on a shift within the bacteria soil community, including specific enrichment of Gemmatimonas and Sphingomonas. PMID:24871319

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.

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.

Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach.

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Xing Liu

Full Text Available BACKGROUND: Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. METHODOLOGY/PRINCIPAL FINDINGS: Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon and richness (S(Chao1 indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM and total nitrogen (TN but positively with electrical conductivity (EC. Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. CONCLUSIONS: Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar

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.

Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing

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Cuicui Xiao

2016-07-01

Full Text Available Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700 clustered into 10,365 operational taxonomic units (OTUs; 97% identity, representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. Smooth rarefaction curves were suggestive of plaque microbial diversity. α diversity analysis showed that healthy plaque microbial diversity exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups and that group members were relatively constant, only showing differences in abundance. Analysis of composition differences identified 10 health-related and 21 caries-related genera. Key genera (27 that potentially contributed to plaque microbiota distributions between groups were identified. Finally, co-occurrence network analysis and function prediction were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

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

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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

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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.

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

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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.

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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.

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 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

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.

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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.

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

16 CFR 0.9 - Organization structure.

Science.gov (United States)

2010-01-01

... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Organization structure. 0.9 Section 0.9 Commercial Practices FEDERAL TRADE COMMISSION ORGANIZATION, PROCEDURES AND RULES OF PRACTICE ORGANIZATION § 0.9 Organization structure. The Federal Trade Commission comprises the following principal units...

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.

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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.

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

Structure and Structure-activity Relationship of Functional Organic Molecules

Institute of Scientific and Technical Information of China (English)

2011-01-01

@@ Research theme The group is made up of junior scientists from the State Key Laboratory of Elemento-organic Chemistry, Nankai University.The scientists focus their studis on the structure and structure-activity relationship of functional organic molecules not only because it has been the basis of their research, but also because the functional study of organic compounds is now a major scientific issue for organic chemists around the world.

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.

Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies

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Davide Francioli

2016-09-01

Full Text Available Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization, carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria and Zygomycota that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil

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.

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.

Bacterial flora-typing with targeted, chip-based Pyrosequencing

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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

Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy.

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Hu, H; Johani, K; Gosbell, I B; Jacombs, A S W; Almatroudi, A; Whiteley, G S; Deva, A K; Jensen, S; Vickery, K

2015-09-01

Hospital-associated infections cause considerable morbidity and mortality, and are expensive to treat. Organisms causing these infections can be sourced from the inanimate environment around a patient. Could the difficulty in eradicating these organisms from the environment be because they reside in dry surface biofilms? The intensive care unit (ICU) of a tertiary referral hospital was decommissioned and the opportunity to destructively sample clinical surfaces was taken in order to investigate whether multidrug-resistant organisms (MDROs) had survived the decommissioning process and whether they were present in biofilms. The ICU had two 'terminal cleans' with 500 ppm free chlorine solution; items from bedding, surrounds, and furnishings were then sampled with cutting implements. Sections were sonicated in tryptone soya broth and inoculated on to chromogenic plates to demonstrate MDROs, which were confirmed with the Vitek2 system. Genomic DNA was extracted directly from ICU samples, and subjected to polymerase chain reaction (PCR) for femA to detect Staphylococcus aureus and the microbiome by bacterial tag-encoded FLX amplicon pyrosequencing. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were performed on environmental samples. Multidrug-resistant bacteria were cultured from 52% (23/44) of samples cultured. S. aureus PCR was positive in 50%. Biofilm was demonstrated in 93% (41/44) of samples by CLSM and/or SEM. Pyrosequencing demonstrated that the biofilms were polymicrobial and contained species that had multidrug-resistant strains. Dry surface biofilms containing MDROs are found on ICU surfaces despite terminal cleaning with chlorine solution. How these arise and how they might be removed requires further study. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA

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Swathi Anuradha Turlapati

2015-02-01

Full Text Available The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham MA. Thirty soil samples (3 treatments x 2 soil horizons x 5 subplots were collected in 2009 from untreated (control, low nitrogen-amended (LN; 50 kg NH4NO3 ha-1 yr-1 and high nitrogen-amended (HN; 150 kg NH4NO3 ha-1 yr-1 plots. PCR-amplified partial 16S rDNA sequences made from soil DNA were subjected to pyrosequencing (Turlapati et al., 2013 and analyses using oligotyping. The parameters M (the minimum count of the most abundant unique sequence in an oligotype and s (minimum number of samples in which an oligotype is expected to be present had to be optimized for forest soils because of high diversity and the presence of rare organisms. Comparative analyses of the pyrosequencing data by oligotyping and OTU (Operational Taxonomic Unit clustering tools indicated that the former yields more refined units of taxonomy with sequence similarity of ≥99.5%. Sequences affiliated with 4 new phyla and 73 genera were identified in the present study as compared to 27 genera reported earlier from the same data (Turlapati et al., 2013. Significant rearrangements in the bacterial community structure were observed with N-amendments revealing the presence of additional genera in N-amended plots with the absence of some that were present in the control plots. Permutational MANOVA analyses indicated significant variation associated with soil horizon and N treatment for a majority of the phyla. In most cases soil horizon partitioned more variation relative to treatment and treatment effects were more evident for the organic horizon. Mantel test results for organic soil showed significant positive correlations between bacterial communities and most soil parameters including NH4 and NO3. In mineral soil, correlations were seen only with pH, NH4 and NO3. Regardless of the pipeline used, a major hindrance for such a study remains to be the lack of reference

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.

Science.gov (United States)

Sergeeva, Ekaterina M; Shcherban, Andrey B; Adonina, Irina G; Nesterov, Michail A; Beletsky, Alexey V; Rakitin, Andrey L; Mardanov, Andrey V; Ravin, Nikolai V; Salina, Elena A

2017-11-14

The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat. Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread

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

Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing.

Science.gov (United States)

Delgado, Susana; Rachid, Caio T C C; Fernández, Elena; Rychlik, Tomasz; Alegría, Angel; Peixoto, Raquel S; Mayo, Baltasar

2013-10-01

Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate

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

Directory of Open Access Journals (Sweden)

Eiko E Kuramae

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

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.

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.

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.

Organizational structure in process-based organizations

NARCIS (Netherlands)

Vanhaverbeke, W.P.M.; Torremans, H.P.M.

1999-01-01

This paper investigates the role of the organization structure in process-based organizations. We argue that companies cannot be designed upon organizational processes only or that process management can be simply imposed as an additional structural dimension on top of the existing functional or

Real-time monitoring of methane oxidation in a simulated landfill cover soil and MiSeq pyrosequencing analysis of the related bacterial community structure.

Science.gov (United States)

Xing, Zhilin; Zhao, Tiantao; Gao, Yanhui; He, Zhi; Zhang, Lijie; Peng, Xuya; Song, Liyan

2017-10-01

Real-time CH 4 oxidation in a landfill cover soil was studied using automated gas sampling that determined biogas (CH 4 and CO 2 ) and O 2 concentrations at various depths in a simulated landfill cover soil (SLCS) column reactor. The real-time monitoring system obtained more than 10,000 biogas (CH 4 and CO 2 ) and O 2 data points covering 32 steady states of CH 4 oxidation with 32 different CH 4 fluxes (0.2-125mol·m -2 ·d -1 ). The kinetics of CH 4 oxidation at different depths (0-20cm, 20-40cm, and 40-60cm) of SLCS were well fit by a CH 4 -O 2 dual-substrate model based on 32 values (averaged, n=5-15) of equilibrated CH 4 concentrations. The quality of the fit (R 2 ranged from 0.90 to 0.96) was higher than those reported in previous studies, which suggests that real time monitoring is beneficial for CH 4 oxidation simulations. MiSeq pyrosequencing indicated that CH 4 flux events changed the bacterial community structure (e.g., increased the abundance of Bacteroidetes and Methanotrophs) and resulted in a relative increase in the amount of type I methanotrophs (Methylobacter and Methylococcales) and a decrease in the amount of type II methanotrophs (Methylocystis). Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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

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Juan M. Arroyo

2013-12-01

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

The Design of Project Management Structural Organization

OpenAIRE

Dumitru Constantinescu; Cristian Etegan

2007-01-01

The relationships organization-suppliers-customers have recently known major changes in the structure of services and have made the organization develop its managerial and professional competencies in order to do projects. The qualified organization is the most trust-worthy in the process of doing a project. The participation of an organization in doing projects depends on a multitude of factors. Out of these factors, the structural organization comes forth, as it represents the variable with...

Electricity generation and microbial community structure of air-cathode microbial fuel cells powered with the organic fraction of municipal solid waste and inoculated with different seeds

KAUST Repository

El-Chakhtoura, Joline

2014-08-01

The organic fraction of municipal solid waste (OFMSW), normally exceeding 60% of the waste stream in developing countries, could constitute a valuable source of feed for microbial fuel cells (MFCs). This study tested the start-up of two sets of OFMSW-fed air-cathode MFCs inoculated with wastewater sludge or cattle manure. The maximum power density obtained was 123±41mWm-2 in the manure-seeded MFCs and 116±29mWm-2 in the wastewater-seeded MFCs. Coulombic efficiencies ranged between 24±5% (manure-seeded MFCs) and 23±2% (wastewater-seeded MFCs). Chemical oxygen demand removal was >86% in all the MFCs and carbohydrate removal >98%. Microbial community analysis using 16S rRNA gene pyrosequencing demonstrated the dominance of the phylum Firmicutes (67%) on the anode suggesting the possible role of members of this phylum in electricity generation. Principal coordinate analysis showed that the microbial community structure in replicate MFCs converged regardless of the inoculum source. This study demonstrates efficient electricity production coupled with organic treatment in OFMSW-fueled MFCs inoculated with manure or wastewater. © 2014 Elsevier Ltd.

Electricity generation and microbial community structure of air-cathode microbial fuel cells powered with the organic fraction of municipal solid waste and inoculated with different seeds

KAUST Repository

El-Chakhtoura, Joline; El-Fadel, Mutasem E.; Rao, Hari Ananda; Li, Dong; Ghanimeh, Sophia A.; Saikaly, Pascal

2014-01-01

The organic fraction of municipal solid waste (OFMSW), normally exceeding 60% of the waste stream in developing countries, could constitute a valuable source of feed for microbial fuel cells (MFCs). This study tested the start-up of two sets of OFMSW-fed air-cathode MFCs inoculated with wastewater sludge or cattle manure. The maximum power density obtained was 123±41mWm-2 in the manure-seeded MFCs and 116±29mWm-2 in the wastewater-seeded MFCs. Coulombic efficiencies ranged between 24±5% (manure-seeded MFCs) and 23±2% (wastewater-seeded MFCs). Chemical oxygen demand removal was >86% in all the MFCs and carbohydrate removal >98%. Microbial community analysis using 16S rRNA gene pyrosequencing demonstrated the dominance of the phylum Firmicutes (67%) on the anode suggesting the possible role of members of this phylum in electricity generation. Principal coordinate analysis showed that the microbial community structure in replicate MFCs converged regardless of the inoculum source. This study demonstrates efficient electricity production coupled with organic treatment in OFMSW-fueled MFCs inoculated with manure or wastewater. © 2014 Elsevier Ltd.

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

Science.gov (United States)

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

2015-12-01

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

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment

KAUST Repository

Jeong, Sanghyun; Cho, Kyungjin; Bae, Hyokwan; Keshvardoust, Pejhman; Rice, Scott A.; Vigneswaran, Saravanamuthu; Lee, Seockheon; Leiknes, TorOve

2016-01-01

Membrane bioreactors (MBRs) were operated on-site for 56 d with different powdered activated carbon (PAC) dosages of 0, 1.5 and 5.0 g/L to pretreat seawater for reverse osmosis desalination. It was hypothesized that PAC would stimulate adsorption and biological degradation of organic compounds. The microbial communities responsible for biofouling on microfiltration (MF) membranes and biological organic removal in MBR were assessed using terminal restriction fragment length polymorphism fingerprinting and 454-pyrosequencing. The PAC addition improved assimilable organic carbon removal (53-59%), and resulted in reduced biofouling development on MF (> 50%) with only a marginal development in trans-membrane pressure. Interestingly, the bacterial community composition was significantly differentiated by the PAC addition. Cyanobacterium, Pelagibaca and Maricoccus were dominant in the PAC-free conditions, while Thiothrix and Sphingomonas were presumably responsible for the better reactor performances in PAC-added conditions. In contrast, the archaeal communities were consistent with predominance of Candidatus Nitrosopumilus. These data therefore show that the addition of PAC can improve MBR performance by developing different bacterial species, controlling AOC and associated biofouling on the membranes.

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment

KAUST Repository

Jeong, Sanghyun

2016-03-03

Membrane bioreactors (MBRs) were operated on-site for 56 d with different powdered activated carbon (PAC) dosages of 0, 1.5 and 5.0 g/L to pretreat seawater for reverse osmosis desalination. It was hypothesized that PAC would stimulate adsorption and biological degradation of organic compounds. The microbial communities responsible for biofouling on microfiltration (MF) membranes and biological organic removal in MBR were assessed using terminal restriction fragment length polymorphism fingerprinting and 454-pyrosequencing. The PAC addition improved assimilable organic carbon removal (53-59%), and resulted in reduced biofouling development on MF (> 50%) with only a marginal development in trans-membrane pressure. Interestingly, the bacterial community composition was significantly differentiated by the PAC addition. Cyanobacterium, Pelagibaca and Maricoccus were dominant in the PAC-free conditions, while Thiothrix and Sphingomonas were presumably responsible for the better reactor performances in PAC-added conditions. In contrast, the archaeal communities were consistent with predominance of Candidatus Nitrosopumilus. These data therefore show that the addition of PAC can improve MBR performance by developing different bacterial species, controlling AOC and associated biofouling on the membranes.

Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments.

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Meiying Xu

Full Text Available Polybrominated diphenyl ethers (PBDEs can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32 and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.

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

Minerals with metal-organic framework structures.

Science.gov (United States)

Huskić, Igor; Pekov, Igor V; Krivovichev, Sergey V; Friščić, Tomislav

2016-08-01

Metal-organic frameworks (MOFs) are an increasingly important family of advanced materials based on open, nanometer-scale metal-organic architectures, whose design and synthesis are based on the directed assembly of carefully designed subunits. We now demonstrate an unexpected link between mineralogy and MOF chemistry by discovering that the rare organic minerals stepanovite and zhemchuzhnikovite exhibit structures found in well-established magnetic and proton-conducting metal oxalate MOFs. Structures of stepanovite and zhemchuzhnikovite, exhibiting almost nanometer-wide and guest-filled apertures and channels, respectively, change the perspective of MOFs as exclusively artificial materials and represent, so far, unique examples of open framework architectures in organic minerals.

Tree-Structured Digital Organisms Model

Science.gov (United States)

Suzuki, Teruhiko; Nobesawa, Shiho; Tahara, Ikuo

Tierra and Avida are well-known models of digital organisms. They describe a life process as a sequence of computation codes. A linear sequence model may not be the only way to describe a digital organism, though it is very simple for a computer-based model. Thus we propose a new digital organism model based on a tree structure, which is rather similar to the generic programming. With our model, a life process is a combination of various functions, as if life in the real world is. This implies that our model can easily describe the hierarchical structure of life, and it can simulate evolutionary computation through mutual interaction of functions. We verified our model by simulations that our model can be regarded as a digital organism model according to its definitions. Our model even succeeded in creating species such as viruses and parasites.

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance.

Science.gov (United States)

Riber, Leise; Poulsen, Pernille H B; Al-Soud, Waleed A; Skov Hansen, Lea B; Bergmark, Lasse; Brejnrod, Asker; Norman, Anders; Hansen, Lars H; Magid, Jakob; Sørensen, Søren J

2014-10-01

We investigated immediate and long-term effects on bacterial populations of soil amended with cattle manure, sewage sludge or municipal solid waste compost in an ongoing agricultural field trial. Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil bacterial community structure was investigated using 16S rRNA amplicon pyrosequencing. Bacterial community structure at phylum level remained mostly unaffected. Actinobacteria, Proteobacteria and Chloroflexi were the most prevalent phyla significantly responding to sampling time. Seasonal changes seemed to prevail with decreasing bacterial richness in week 9 followed by a significant increase in week 29 (springtime). The Pseudomonas population richness seemed temporarily affected by fertilizer treatments, especially in sludge- and compost-amended soils. To explain these changes, prevalence of antibiotic- and mercury-resistant pseudomonads was investigated. Fertilizer amendment had a transient impact on the resistance profile of the soil community; abundance of resistant isolates decreased with time after fertilizer application, but persistent strains appeared multiresistant, also in unfertilized soil. Finally, the ability of a P. putida strain to take up resistance genes from indigenous soil bacteria by horizontal gene transfer was present only in week 0, indicating a temporary increase in prevalence of transferable antibiotic resistance genes. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Re-Ordering Structural Dimensions for Nigerian Organizations ...

African Journals Online (AJOL)

The organization structure (OS) reflects the interface of the dimensions of the OS, the model in place and the mix of determinants of OS. This paper focuses on the organization structure (OS) to find out, not just the consistency of the structural properties with the OS but also the potentials of OS oriented towards the realization ...

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA.

Science.gov (United States)

Turlapati, Swathi A; Minocha, Rakesh; Long, Stephanie; Ramsdell, Jordan; Minocha, Subhash C

2015-01-01

The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham, MA, USA. Thirty soil samples (3 treatments × 2 soil horizons × 5 subplots) were collected in 2009 from untreated (control), low nitrogen-amended (LN; 50 kg NH4NO3 ha(-1) yr(-1)) and high nitrogen-amended (HN; 150 kg NH4NO3 ha(-1) yr(-1)) plots. PCR-amplified partial 16S rRNA gene sequences made from soil DNA were subjected to pyrosequencing (Turlapati et al., 2013) and analyses using oligotyping. The parameters M (the minimum count of the most abundant unique sequence in an oligotype) and s (the minimum number of samples in which an oligotype is expected to be present) had to be optimized for forest soils because of high diversity and the presence of rare organisms. Comparative analyses of the pyrosequencing data by oligotyping and operational taxonomic unit clustering tools indicated that the former yields more refined units of taxonomy with sequence similarity of ≥99.5%. Sequences affiliated with four new phyla and 73 genera were identified in the present study as compared to 27 genera reported earlier from the same data (Turlapati et al., 2013). Significant rearrangements in the bacterial community structure were observed with N-amendments revealing the presence of additional genera in N-amended plots with the absence of some that were present in the control plots. Permutational MANOVA analyses indicated significant variation associated with soil horizon and N treatment for a majority of the phyla. In most cases soil horizon partitioned more variation relative to treatment and treatment effects were more evident for the organic (Org) horizon. Mantel test results for Org soil showed significant positive correlations between bacterial communities and most soil parameters including NH4 and NO3. In mineral soil, correlations were seen only with pH, NH4, and NO3. Regardless of the pipeline used, a major hindrance for such a study remains to be the lack

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

Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

Science.gov (United States)

Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

2015-10-30

The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.

Low acetate concentrations favor polyphosphate-accumulating organisms over glycogen-accumulating organisms in enhanced biological phosphorus removal from wastewater.

Science.gov (United States)

Tu, Yunjie; Schuler, Andrew J

2013-04-16

Glycogen-accumulating organisms (GAOs) are thought to compete with polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) wastewater treatment systems. A laboratory sequencing batch reactor (SBR) was operated for one year to test the hypothesis that PAOs have a competitive advantage at low acetate concentrations, with a focus on low pH conditions previously shown to favor GAOs. PAOs dominated the system under conventional SBR operation with rapid acetate addition (producing high in-reactor concentrations) and pH values of 7.4-8.4. GAOs dominated when the pH was decreased (6.4-7.0). Decreasing the acetate addition rate led to very low reactor acetate concentrations, and PAOs recovered, supporting the study hypothesis. When the acetate feed rate was increased, EBPR failed again. Dominant PAOs and GAOs were Candidatus Accumulibacter phosphatis and Defluviicoccus Cluster 2, respectively, according to fluorescent in situ hybridization and 454 pyrosequencing. Surprisingly, GAOs were not the immediate causes of PAO failures, based on functional and population measurements. Pyrosequencing results suggested Dechloromonas and Tetrasphaera spp. may have also been PAOs, and additional potential GAOs were also identified. Full-scale systems typically have lower in-reactor acetate concentrations than laboratory SBRs, and so, previous laboratory studies may have overestimated the practical importance of GAOs as causes of EBPR failure.

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.

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

Science.gov (United States)

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

2014-01-01

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

STRUCTURE AND COOPTATION IN ORGANIZATION NETWORK

Directory of Open Access Journals (Sweden)

Valéria Riscarolli

2007-10-01

Full Text Available Business executive are rethinking business concept, based on horizontalization principles. As so, most organizational functions are outsourced, leading the enterprise to build business through a network of organizations. Here we study the case of Cia Hering’s network of organizations, a leader in knit apparel segment in Latin America (IEMI, 2004, looking at the network’s structure and levels of cooptation. A theoretical model was used using Quinn et al. (2001 “sun ray” network structure as basis to analyze the case study. Main results indicate higher degree of structural conformity, but incipient degree of coopetation in the network.

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.

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.

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

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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.

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...

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

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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.

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.

Science.gov (United States)

Peña-Espinoza, Miguel; Thamsborg, Stig M; Demeler, Janina; Enemark, Heidi L

2014-12-15

We describe a case of anthelmintic resistance on one of the largest organic small ruminant farms in Denmark. The flock was established in 2007 by purchase of animals from other Danish farms and had history of clinical parasitism, high mortality of young stock and anthelmintic treatment failure. In October 2011, 40 lambs and 40 kids were selected for a faecal egg count reduction test (FECRT) with fenbendazole (FBZ), ivermectin (IVM), moxidectin (MOX) and levamisole (LEV). Lambs were treated with the recommended sheep dose of each product while kids received the sheep dose of IVM, 1.5× sheep dose of MOX and 2× sheep dose of FBZ and LEV. Untreated lambs and kids were also included and three methods for calculating faecal egg count (FEC) reduction were compared. In a subsequent investigation, a controlled efficacy test (CET) with FBZ and IVM was performed in lambs infected with Haemonchus contortus 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 reduction was detected in untreated kids. After FBZ treatments, FEC reductions in lambs and kids ranged from 15 to 54% and 49-56%, respectively, according to the different calculation methods. Post IVM treatments, FEC reductions in lambs and kids varied between 71-90% and 81-83%, correspondingly. LEV and MOX reduced FECs by 98-100% in both species. In the CET, FBZ reduced H. contortus worm counts by 52-56% and no reduction in T. colubriformis counts were detected after treatment. IVM eliminated 100% of H. contortus and reduced T. colubriformis counts by 84-92%, according to different calculation methods. Pyrosequencing of isolated H. contortus revealed increased frequencies of the BZ resistance-related SNP in codon 200 of the β-tubulin isotype 1 gene

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...

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

Science.gov (United States)

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

2015-01-01

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

Structural hierarchy in flow-aligned hexagonally self-organized microphases with parallel polyelectrolytic structures

NARCIS (Netherlands)

Ruotsalainen, T; Torkkeli, M; Serimaa, R; Makela, T; Maki-Ontto, R; Ruokolainen, J; ten Brinke, G; Ikkala, O; Mäkelä, Tapio; Mäki-Ontto, Riikka

2003-01-01

We report a novel structural hierarchy where a flow-aligned hexagonal self-organized structure is combined with a polyelectrolytic self-organization on a smaller length scale and where the two structures are mutually parallel. Polystyrene-block-poly(4-vinylpyridine) (PS-block-P4VP) is selected with

Structured-gate organic field-effect transistors

International Nuclear Information System (INIS)

Aljada, Muhsen; Pandey, Ajay K; Velusamy, Marappan; Burn, Paul L; Meredith, Paul; Namdas, Ebinazar B

2012-01-01

We report the fabrication and electrical characteristics of structured-gate organic field-effect transistors consisting of a gate electrode patterned with three-dimensional pillars. The pillar gate electrode was over-coated with a gate dielectric (SiO 2 ) and solution processed organic semiconductors producing both unipolar p-type and bipolar behaviour. We show that this new structured-gate architecture delivers higher source-drain currents, higher gate capacitance per unit equivalent linear channel area, and enhanced charge injection (electrons and/or holes) versus the conventional planar structure in all modes of operation. For the bipolar field-effect transistor (FET) the maximum source-drain current enhancements in p- and n-channel mode were >600% and 28%, respectively, leading to p and n charge mobilities with the same order of magnitude. Thus, we have demonstrated that it is possible to use the FET architecture to manipulate and match carrier mobilities of material combinations where one charge carrier is normally dominant. Mobility matching is advantageous for creating organic logic circuit elements such as inverters and amplifiers. Hence, the method represents a facile and generic strategy for improving the performance of standard organic semiconductors as well as new materials and blends. (paper)

Structured-gate organic field-effect transistors

Science.gov (United States)

Aljada, Muhsen; Pandey, Ajay K.; Velusamy, Marappan; Burn, Paul L.; Meredith, Paul; Namdas, Ebinazar B.

2012-06-01

We report the fabrication and electrical characteristics of structured-gate organic field-effect transistors consisting of a gate electrode patterned with three-dimensional pillars. The pillar gate electrode was over-coated with a gate dielectric (SiO2) and solution processed organic semiconductors producing both unipolar p-type and bipolar behaviour. We show that this new structured-gate architecture delivers higher source-drain currents, higher gate capacitance per unit equivalent linear channel area, and enhanced charge injection (electrons and/or holes) versus the conventional planar structure in all modes of operation. For the bipolar field-effect transistor (FET) the maximum source-drain current enhancements in p- and n-channel mode were >600% and 28%, respectively, leading to p and n charge mobilities with the same order of magnitude. Thus, we have demonstrated that it is possible to use the FET architecture to manipulate and match carrier mobilities of material combinations where one charge carrier is normally dominant. Mobility matching is advantageous for creating organic logic circuit elements such as inverters and amplifiers. Hence, the method represents a facile and generic strategy for improving the performance of standard organic semiconductors as well as new materials and blends.

Organization structure of a basic school of arts

OpenAIRE

Sinkulová, Iveta

2012-01-01

TITLE: Organization Structure of a Basic School of Arts AUTHOR: Iveta Sinkulová ABSTRACT: My bachelor thesis "Organization Structure of a Basic School of Arts" sets a goal to research which organization structures are applied at basic schools of arts, how the jobs of headmaster and heads of departments are incorporated into the Org Chart and which tasks are delegated to them in terms of the management of teaching process. The first thing performed was descriptive research. Then the work of de...

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

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

Science.gov (United States)

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

2014-09-01

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

Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.

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Lance B Price

Full Text Available BACKGROUND: Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. METHODOLOGY/PRINCIPAL FINDINGS: We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007 and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. CONCLUSIONS/SIGNIFICANCE: The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.

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

Science.gov (United States)

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

2015-08-01

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

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.

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

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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.

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.

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

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Elianne Egge

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

The Analysis of a Microbial Community in the UV/O3-Anaerobic/Aerobic Integrated Process for Petrochemical Nanofiltration Concentrate (NFC Treatment by 454-Pyrosequencing.

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Chao Wei

Full Text Available In this study, high-throughput pyrosequencing was applied on the analysis of the microbial community of activated sludge and biofilm in a lab-scale UV/O3- anaerobic/aerobic (A/O integrated process for the treatment of petrochemical nanofiltration concentrate (NFC wastewater. NFC is a type of saline wastewater with low biodegradability. From the anaerobic activated sludge (Sample A and aerobic biofilm (Sample O, 59,748 and 51,231 valid sequence reads were obtained, respectively. The dominant phylotypes related to the metabolism of organic compounds, polycyclic aromatic hydrocarbon (PAH biodegradation, assimilation of carbon from benzene, and the biodegradation of nitrogenous organic compounds were detected as genus Clostridium, genera Pseudomonas and Stenotrophomonas, class Betaproteobacteria, and genus Hyphomicrobium. Furthermore, the nitrite-oxidising bacteria Nitrospira, nitrite-reducing and sulphate-oxidising bacteria (NR-SRB Thioalkalivibrio were also detected. In the last twenty operational days, the total Chemical Oxygen Demand (COD and Total Organic Carbon (TOC removal efficiencies on average were 64.93% and 62.06%, respectively. The removal efficiencies of ammonia nitrogen and Total Nitrogen (TN on average were 90.51% and 75.11% during the entire treatment process.

The Analysis of a Microbial Community in the UV/O3-Anaerobic/Aerobic Integrated Process for Petrochemical Nanofiltration Concentrate (NFC) Treatment by 454-Pyrosequencing

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Wei, Chao; He, Wenjie; Wei, Li; Li, Chunying; Ma, Jun

2015-01-01

In this study, high-throughput pyrosequencing was applied on the analysis of the microbial community of activated sludge and biofilm in a lab-scale UV/O3- anaerobic/aerobic (A/O) integrated process for the treatment of petrochemical nanofiltration concentrate (NFC) wastewater. NFC is a type of saline wastewater with low biodegradability. From the anaerobic activated sludge (Sample A) and aerobic biofilm (Sample O), 59,748 and 51,231 valid sequence reads were obtained, respectively. The dominant phylotypes related to the metabolism of organic compounds, polycyclic aromatic hydrocarbon (PAH) biodegradation, assimilation of carbon from benzene, and the biodegradation of nitrogenous organic compounds were detected as genus Clostridium, genera Pseudomonas and Stenotrophomonas, class Betaproteobacteria, and genus Hyphomicrobium. Furthermore, the nitrite-oxidising bacteria Nitrospira, nitrite-reducing and sulphate-oxidising bacteria (NR-SRB) Thioalkalivibrio were also detected. In the last twenty operational days, the total Chemical Oxygen Demand (COD) and Total Organic Carbon (TOC) removal efficiencies on average were 64.93% and 62.06%, respectively. The removal efficiencies of ammonia nitrogen and Total Nitrogen (TN) on average were 90.51% and 75.11% during the entire treatment process. PMID:26461260

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

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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).

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

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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.

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

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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.

Interface Structure of MoO3 on Organic Semiconductors

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White, Robin T.; Thibau, Emmanuel S.; Lu, Zheng-Hong

2016-01-01

We have systematically studied interface structure formed by vapor-phase deposition of typical transition metal oxide MoO3 on organic semiconductors. Eight organic hole transport materials have been used in this study. Ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy are used to measure the evolution of the physical, chemical and electronic structure of the interfaces at various stages of MoO3 deposition on these organic semiconductor surfaces. For the interface physical structure, it is found that MoO3 diffuses into the underlying organic layer, exhibiting a trend of increasing diffusion with decreasing molecular molar mass. For the interface chemical structure, new carbon and molybdenum core-level states are observed, as a result of interfacial electron transfer from organic semiconductor to MoO3. For the interface electronic structure, energy level alignment is observed in agreement with the universal energy level alignment rule of molecules on metal oxides, despite deposition order inversion. PMID:26880185

Matrix Organizational Structure and Its Effects Upon Education Organizations.

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Yates, James R.

Applying matrix organizational structure to the organization of special education services is the focus of this paper. Beginning with a list of ways in which educational organizations differ from business or military organizations, the author warns that educators must be cautious when transferring organizational structures from other disciplines…

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

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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.

From Virtual Organization to E-Business: Transformational Structuration

OpenAIRE

James J. Lee; Bandula Jayatilaka; Ben B. Kim; Ted E. Lee; Pairin Katerattanakul; Soongoo Hong

2010-01-01

This article shows how the technical hype of 1990s has been transformed into the e-business organizations at the beginning of the 21st century. The authors took an interpretive stance in this study, grounded theory, and investigated the ontology of virtual organization by the metaphorical analysis. The metaphorical analysis adopted in this study provides the analytical power to conceptualize the social structure of virtual organization in the context of structuration theory with the process o...

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...

STRUCTURIZATION OF COMPETITIVE CAPACITY OF TRADE ORGANIZATION

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N. A. Sеrеbrуаkоvа

2015-01-01

Full Text Available The modern consumer market is characterized by a complex of immanent tendencies of development, the competitive relations reflecting specifics inherent in it. These tendencies of development of the competitive environment of the consumer market are in many respects caused by a state and extent of use of competitive capacity of the organizations functioning in this market. This obvious circumstance causes the necessity of complex scientific research of competitive capacity of trade organizations, including its structures, for definition of prospects of its sustainable strategic development. Immanent properties of competitive capacity of trade organization allowed to study in detail its structure, by means of the substantial review of the existing options of its representation and their systematization on specific, element and system signs. In development of specific structure of competitive potential its addition commercial, technological, communication, consumer and image the potentials reflecting functional and branch specifics of activity of trade organization is offered. The system of elements of competitive capacity of trade organization is given by its structure-forming types. It is proved that these elements aren't characterized by strict distribution by types of potentials, and separate from elements are universal, accepted for simultaneous use when forming all types of potential. Allocation of a system sign of structurization of competitive potential was based on situation that "systemacity" has to be provided not so much with hierarchy of hierarchy of types and elements of potential, their interrelations, how many possibility of the accounting of various classification signs allowing to typify competitive potential as system integrity, regardless of its separate types. Those signs were the stage of a demand and level of use in economic activity, economic feasibility of existence of unrealized potential, the origin nature.

Principles of disaster management lesson. 12: structuring organizations.

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Cuny, F C

2001-01-01

This lesson discusses various structures for organizations that have functional roles in disaster responses, relief, and/or management activities. It distinguishes between pyramidal and matrix structures, and notes the advantages and disadvantages of each in relation to disasters. Span of control issues are dissected including the impact of the "P" factor on the performance of disaster managers and workers including its relationship to the coordination and control function. The development of a Table of Organization and how it relates to departmentalization within an organization also is provided.

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

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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.

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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

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

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

2009-12-02

. Pyrosequencing is an attractive approach to gain access to genes in the biosynthesis of bio-active natural products from insects and other organisms, for which the genome sequence is not known. Based on analysis of the Z. filipendulae transcriptome, promising gene candidates for biosynthesis of cyanogenic glucosides was identified, and the suitability of Z. filipendulae as a model system for cyanogenesis in insects is evident.

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

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Jensen Niels

2009-12-01

convergent between plants and insects. Conclusion Pyrosequencing is an attractive approach to gain access to genes in the biosynthesis of bio-active natural products from insects and other organisms, for which the genome sequence is not known. Based on analysis of the Z. filipendulae transcriptome, promising gene candidates for biosynthesis of cyanogenic glucosides was identified, and the suitability of Z. filipendulae as a model system for cyanogenesis in insects is evident.

Emission Characteristics of Organic Light-Emitting Diodes and Organic Thin-Films with Planar and Corrugated Structures

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Mao-Kuo Wei

2010-04-01

Full Text Available In this paper, we review the emission characteristics from organic light-emitting diodes (OLEDs and organic molecular thin films with planar and corrugated structures. In a planar thin film structure, light emission from OLEDs was strongly influenced by the interference effect. With suitable design of microcavity structure and layer thicknesses adjustment, optical characteristics can be engineered to achieve high optical intensity, suitable emission wavelength, and broad viewing angles. To increase the extraction efficiency from OLEDs and organic thin-films, corrugated structure with micro- and nano-scale were applied. Microstructures can effectively redirects the waveguiding light in the substrate outside the device. For nanostructures, it is also possible to couple out the organic and plasmonic modes, not only the substrate mode.

Community structure, population dynamics and diversity of fungi in a full-scale membrane bioreactor (MBR) for urban wastewater treatment.

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Maza-Márquez, P; Vilchez-Vargas, R; Kerckhof, F M; Aranda, E; González-López, J; Rodelas, B

2016-11-15

Community structure, population dynamics and diversity of fungi were monitored in a full-scale membrane bioreactor (MBR) operated throughout four experimental phases (Summer 2009, Autumn 2009, Summer 2010 and Winter, 2012) under different conditions, using the 18S-rRNA gene and the intergenic transcribed spacer (ITS2-region) as molecular markers, and a combination of temperature-gradient gel electrophoresis and 454-pyrosequencing. Both total and metabolically-active fungal populations were fingerprinted, by amplification of molecular markers from community DNA and retrotranscribed RNA, respectively. Fingerprinting and 454-pyrosequencing evidenced that the MBR sheltered a dynamic fungal community composed of a low number of species, in accordance with the knowledge of fungal diversity in freshwater environments, and displaying a medium-high level of functional organization with few numerically dominant phylotypes. Population shifts were experienced in strong correlation with the changes of environmental variables and operation parameters, with pH contributing the highest level of explanation. Phylotypes assigned to nine different fungal Phyla were detected, although the community was mainly composed of Ascomycota, Basidiomycota and Chytridiomycota/Blastocladiomycota. Prevailing fungal phylotypes were affiliated to Saccharomycetes and Chytridiomycetes/Blastocladiomycetes, which displayed antagonistic trends in their relative abundance throughout the experimental period. Fungi identified in the activated sludge were closely related to genera of relevance for the degradation of organic matter and trace-organic contaminants, as well as genera of dimorphic fungi potentially able to produce plant operational issues such as foaming or biofouling. Phylotypes closely related to genera of human and plant pathogenic fungi were also detected. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

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Lisa-Maree Gulino

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

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

Science.gov (United States)

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

2013-01-01

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

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.

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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

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

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Azhahianambi Palavesam

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

Rapid and accurate pyrosequencing of angiosperm plastid genomes

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

2006-01-01

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

Rapid and accurate pyrosequencing of angiosperm plastid genomes

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Farmerie William G

2006-08-01

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

[Volunteer satisfaction: Internal structure and relationship with permanence in organizations].

Science.gov (United States)

Vecina Jiménez, M L; Chacón Fuertes, Fernando; Sueiro Abad, Manuel J

2009-02-01

Volunteer satisfaction: Internal structure and relationship with permanence in organizations. The concept of satisfaction is considered theoretically relevant in practically all the studies that have investigated the factors that influence the permanence of volunteer participation in organizations. However, the practical results are not conclusive, perhaps due to the wide range of ways in which the concept is understood and measured. The object of this study is: to analyse the internal structure of satisfaction and to verify its relationship with volunteer duration in organizations. The results of the factor analysis yield a three-factor structure: Satisfaction with the management of the organization, Satisfaction with the tasks, Satisfaction of motivations. The three factors allow us to differentiate between individuals who remain in the organization for a period of 12 consecutive months, and those who leave earlier. The results of structural equation model analysis show that the relationship between satisfaction and the length of time that volunteers stay with the organization is affected by the intention to remain.

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 ...

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

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Özgül Inceoğlu

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

Scale and structure of capitated physician organizations in California.

Science.gov (United States)

Rosenthal, M B; Frank, R G; Buchanan, J L; Epstein, A M

2001-01-01

Physician organizations in California broke new ground in the 1980s by accepting capitated contracts and taking on utilization management functions. In this paper we present new data that document the scale, structure, and vertical affiliations of physician organizations that accept capitation in California. We provide information on capitated enrollment, the share of revenue derived by physician organizations from capitation contracts, and the scope of risk sharing with health maintenance organizations (HMOs). Capitation contracts and risk sharing dominate payment arrangements with HMOs. Physician organizations appear to have responded to capitation by affiliating with hospitals and management companies, adopting hybrid organizational structures, and consolidating into larger entities.

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.

Structures in plasmas and their self-organizations

International Nuclear Information System (INIS)

Yoshida, Zensho

1989-01-01

This paper is a concise review of the physics of structures. The progress of the structure theory was motivated by the appearances of many different ordered structures that are self-organized through spontaneous dynamics. For typical examples in plasma physics, cited are the MHD equilibria (Taylor relaxed state), the ion acoustic solitons, and the van Kampen modes of continuous-spectrum Langmuir waves. A static theory for the intrinsic structures is developed to clarify the basic difference between the classical orders and the self-organized structures. In linear models, an intrinsic structure is characterized by a singular spectrum of a certain eigenvalue problem. The Taylor relaxed state is characterized by the continuum of the point spectra of the rotational operator. The general MHD equilibrium is related to a nonlinear eigenvalue problem. The soliton is a nonlinear eigenfunction of the Helmholtz-type Bohm equation. The variational expression of an intrinsic structure is characterized by restrictive functionals, which in a dynamical theory, is related to selective conservations. The Taylor relaxed state is obtained by minimizing the magnetic-field energy with conserving the magnetic helicity. This selective dissipation occurs in the fluctuations of kink modes. The soliton is self-organized by the dissipation of the Hamiltonian with keeping the energy approximately constant. The principle of the selective dissipation is logically a generalization of the ergodic hypothesis for the classical order and could be proved in a rigorous way by analyzing the attractor of the dynamical systems, just as the proof the ergodic theorem is obtained by the time-asymptotic analysis of a class of semigroups. (J.P.N.) 85 refs

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.

Differently Structured Advance Organizers Lead to Different Initial Schemata and Learning Outcomes

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Gurlitt, Johannes; Dummel, Sebastian; Schuster, Silvia; Nuckles, Matthias

2012-01-01

Does the specific structure of advance organizers influence learning outcomes? In the first experiment, 48 psychology students were randomly assigned to three differently structured advance organizers: a well-structured, a well-structured and key-concept emphasizing, and a less structured advance organizer. These were followed by a sorting task, a…

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

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Estelle Silvia Kilias

2014-11-01

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

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

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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...

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

Science.gov (United States)

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

2015-08-01

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

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.

Demand structure and willingness to pay for organic dairy products

DEFF Research Database (Denmark)

Smed, Sinne

2005-01-01

This paper analyses if the introduction of a new and “low fat” organic variety of fluid milk has any effect on consumers’ valuation of organic milk in general and can rewind the stagnating trend in the demand for organic milk. In order to analyse this, the consumers’ purchasing structure was anal......This paper analyses if the introduction of a new and “low fat” organic variety of fluid milk has any effect on consumers’ valuation of organic milk in general and can rewind the stagnating trend in the demand for organic milk. In order to analyse this, the consumers’ purchasing structure...... was analysed and it was found that consumers first chose between different types of milk and secondly, decided of whether this milk was organic or conventional. Elasticities indicated a greater temporary flexibility in the demand structure and a permanent change of substitution patterns through...

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

Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama

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Zachary Senwo

2011-07-01

Full Text Available Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa, potato (Solanum tuberosum, onion (Allium cepa L, broccoli (Brassica oleracea var. botrytis and Tall fescue pasture grass (Festuca arundinacea. Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU at 3% dissimilarity level (roughly corresponding to the bacterial species level at 0–10 cm (581.7–770.0 compared to 10–20 cm (563.3–727.7 soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7; whereas the lowest OTUs found at 10–20 cm were under potato (563.3. The predominant phyla (85% in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria, and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more

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.

Nitrosonium complexes of organic compounds. Structure and reactivity

International Nuclear Information System (INIS)

Borodkin, Gennady I; Shubin, Vyacheslav G

2001-01-01

Data on the structures and reactivities of nitrosonium complexes of organic compounds are systematised and generalised. The characteristic features of the electronic structure of the NO + cation are responsible for a wide structural variety of nitrosonium complexes. Reactions of nitrosonium complexes are described. The bibliography includes 172 references.

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.

PLAN FOR PERFORMANCE ADMINISTRATION IN PYRAMIDAL STRUCTURE ORGANIZATIONS

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Domingo Alarcón Ortiz

2013-11-01

Full Text Available Performance administration has become a current strategy in evaluating management within organizations, but its implementation often lacks an action plan, resulting from the valuation of climate and leadership styles embedded in the culture of the organization. This paper proposes a model action plan for performance management, which has been implemented, executed and evaluated in pyramidal organizational structure organizations where a diagnosis of the cultural climate and leadership styles recurring in the organization have been previously made.

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.

Analyze Of Interrelation Between Knowledge Management And Organizatıonal Structure Of Organization

OpenAIRE

MLÁDKOVÁ, Ludmila

2011-01-01

The aim of the article is to discuss interrelation between knowledge management and organizational structure of organization. Organizational structure is a backbone of the organization. Type of organizational structure used has strong impact on everyday life of organization and influences all its activities, including knowledge management. From the point of view of knowledge management, three basic groups of organizational structures can be identified in organizations; top down structures, bo...

Gender Structure and Spatial Organization

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Minoosh Sadoughianzadeh

2013-11-01

Full Text Available As a contribution to the widespread debate on the “gender reading” of the “built environment,” this article aims to situate the subject in a new context, the Iranian society. To depict the subject, two distinct traditional architectures of the region, associated with their respective socio-spatial organizations, have been comparatively explored: the “Introvert” and “Extrovert.” These two almost ageless “Introvert” and “Extrovert” architectures, evolved through centuries in different geographical parts of the country, are spatial patterns aptly illustrating how the “gender structure” of each social organization has contributed to the formation of the relevant “physical space” and, further, how the specific “gender relationships” are pertinently structured within each one of the two types of the spaces. Based on a systematic approach and through concentration on the macro-socio-spatial organization, this article is to explore the gender/space associated variations within either of the social systems they belong to. This perspective is particularly instrumental in pinpointing the Introvert and Extrovert architectures in the context of their social organizations and carefully scrutinizing “gender” and “space” categories as systematically integrated variables.

Challenges of Control in Functional Organization Structures: Example of Outsourcing Sector

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Agnieszka Maciejczyk

2016-07-01

Full Text Available Effective control of an organization is strictly connected with its organization structure. When a company decides to outsource a part of its operations, a new structure is applied. Also, the system of control should be reviewed and adjusted to the new model of business in order to be effective. Usually, the outsourcing companies apply functional organization structure which is the most common way of grouping business activities. The goal of the paper was to point challenges and aspects which should be taken into consideration in order to adapt control systems to new organization structures in case of Business Process Outsourcing and Shared Service Centers. The research was based on literature studies as well as empirical analysis of selected companies from business service centers sector. The key findings of the study suggest that the mechanisms of control differ in Business Process Outsourcing and Shared Service organizations although both base on building trust and relationship. The main challenges of adapting the control system to new conditions comprise people and process related factors such as: knowledge management, control split and owners, new processes flows, virtual teams. Building control system is a process which foundation is a new organization structure.

Nuclear visions enhanced: chromatin structure, organization and dynamics

OpenAIRE

Meshorer, Eran; Herrmann, Harald; Raška, Ivan

2011-01-01

The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

The relationship between family orientation, organization context, organization structure and firm performance

OpenAIRE

Joris Meijaard; Lorraine Uhlaner

2004-01-01

This study focuses on the prediction of three firm performance indicators, sales growth, innovation performance and profitability, on a sample of small and medium-sized firms in the Netherlands. Predictions from agency theory and the resource based view of organizations lead to alternate hypotheses regarding the direct and indirect effects of family ownership and management on firm performance. Other variables in the analysis include various organization structure variables including standard...

Challenges of Control in Functional Organization Structures: Example of Outsourcing Sector

OpenAIRE

Agnieszka Maciejczyk

2016-01-01

Effective control of an organization is strictly connected with its organization structure. When a company decides to outsource a part of its operations, a new structure is applied. Also, the system of control should be reviewed and adjusted to the new model of business in order to be effective. Usually, the outsourcing companies apply functional organization structure which is the most common way of grouping business activities. The goal of the paper was to point challenges and aspects which...

Structural aspects of the evaluation of agent organizations

NARCIS (Netherlands)

Grossi, D.; Dignum, F.P.M.; Dignum, V.; Dastani, M.; Royakkers, L.M.M.; Noriega, P.; Vázquez-Salceda, J.; Boella, G.; Boissier, O.; Dignum, V.; Fornara, N.; Matson, E.

2007-01-01

A multi-agent system can be analyzed and specified as an organization consisting of roles and their relations. The performance of an organization depends on many factors among which the type of its organizational structure, i.e., the set of relations holding between its roles. This work focuses on

Research on Structure Innovation of Agricultural Organization in China’s Southwestern Mountainous Regions

Institute of Scientific and Technical Information of China (English)

2012-01-01

Taking agricultural organization in China’s southwestern mountainous regions as research object,on the basis of analysis of the status quo of agricultural organization development in China’s southwestern mountainous regions,we use related theoretical knowledge on economics and organization science,we probe into the process of innovation and mechanism of action concerning the structure of agricultural organization in China’s southwestern mountainous regions over the past 30 years.Finally we draw several general conclusions regarding structure innovation of agricultural organization in China’s southwestern mountainous regions as follows:first,the structure innovation of agricultural organization,a gradual process,proceeds ceaselessly along with ongoing progress and development of agriculture,and in this process,farmers always play a fundamental role;second,the structure innovation of agricultural organization is affected by many factors,and government institutional arrangement and change in market conditions is undoubtedly the most critical factor;third,the probable evolving direction of structure innovation of agricultural organization includes internal differentiation of the same form of agricultural organization,association of different forms of agricultural organization,and emergence of other forms of agricultural organization.

Organic fertilization alters the community composition of root associated fungi in Pisum sativum

DEFF Research Database (Denmark)

Yu, L.; Nicolaisen, M.; Ravnskov, S.

2013-01-01

Organic fertilization is well known to affect individual functional groups of root associated fungi such as arbuscular mycorrhizal (AM) fungi and root pathogens, but limited information is available on the effect of organic fertilization at the fungal community composition level. The main objective...... of the present study was to examine the response of communities of root associated fungi in Pisum sativum to Protamylasse, an organic fertilizer used in pea production. Plants were grown in pots with field soil amended with four different levels of Protamylasse. 454 pyrosequencing was employed to examine......, the organic fertilizer Protamylasse clearly affects communities of root associated fungi, which seems to be linked to the life strategy of the different functional groups of root associated fungi. --------------------------------------------------------------------------------...

Growth of pseudomorphic structures through organic epitaxy

International Nuclear Information System (INIS)

Kaviyil, Sreejith Embekkat; Sassella, Adele; Borghesi, Alessandro; Campione, Marcello; Su Genbo; He Youping; Chen Chenjia

2012-01-01

The control of molecular orientation in thin solid film phases of organic semiconductors is a basic factor for the exploitation of their physical properties for optoelectronic devices. We compare structural and optical properties of thin films of the organic semiconductor α-quarterthiophene grown by molecular beam epitaxy on different organic substrates. We show how epitactic interactions, characteristic of the surface of organic crystals, can drive the orientation of the crystalline overlayer and the selection of specific polymorphs and new pseudomorphic phases. We identify a key role in this phenomenon played by the marked groove-like corrugations present in some organic crystal surfaces. Since different polymorphs possess rather different performance in terms of, e.g., charge carrier mobility, this strategy is demonstrated to allow for the growth of oriented phases with enhanced physical properties, while keeping the substrate at room temperature. These results provide useful guidelines for the design of technological substrates for organic epitaxy and they substantiate the adoption of an organic epitaxy approach for the fabrication of optoelectronic devices based on thin films of organic semiconductors.

Progress in organic and physical chemistry structures and mechanisms

CERN Document Server

Zaikov, Gennady E; Lobanov, Anton V

2013-01-01

Progress in Organic and Physical Chemistry: Structures and Mechanisms provides a collection of new research in the field of organic and physical properties, including new research on: The physical principles of the conductivity of electrical conducting polymer compounds The dependence on constants of electromagnetic interactions upon electron spacial-energy characteristics Effects of chitosan molecultural weight on rehological behavior of chitosan modified nanoclay at hight hydrated state Bio-structural energy criteria of functional states in normal and pathological conditions Potentiometric study on the international between devalent cations and sodium carboxylates in aqueous solutions Structural characteristic changes in erythrocyte membranes of mice bearing Alzheimer's-like disease caused by the olfactory bulbetomy This volume is intended to provide an overview of new studies and research for engineers, faculty, researchers, and upper-level students in the field of organic and physical chemistry.

Perceptions of the organization's climate: influenced by the organization's structure?

Science.gov (United States)

Grigsby, K A

1991-02-01

Currently, little is known about organizational climates in schools of nursing, and what structural factors are associated with climate variations. The purpose of this study is to describe the organizational structure and climate, and the interrelationship between these factors, in two schools of nursing. Results indicated that the sample organizations exhibited characteristics of both the bureaucratic and professional models of organizational structure, although one school was more closely aligned to the professional model. Organizational climates differed in the two schools, and the school that structurally resembled the professional model had a more facilitative climate. Organizational structure was significantly (p less than .01) related to the climate dimensions of autonomy (r = -.35), work pressure (r = .49), and control (r = .59). The schools differed significantly (p less than .01) on the climate dimensions of administrative support (t = 3.31, df = 54), autonomy (t = 3.30, df = 56), work pressure (t = -4.36, df = 60), and control (t = -6.74, df = 55). Administrative support and autonomy were higher in the school structurally resembling the professional model, and work pressure and control were higher in the school structurally resembling the bureaucratic model.

Virtuous organization: A structural equation modeling approach

Directory of Open Access Journals (Sweden)

Majid Zamahani

2013-02-01

Full Text Available For years, the idea of virtue was unfavorable among researchers and virtues were traditionally considered as culture-specific, relativistic and they were supposed to be associated with social conservatism, religious or moral dogmatism, and scientific irrelevance. Virtue and virtuousness have been recently considered seriously among organizational researchers. The proposed study of this paper examines the relationships between leadership, organizational culture, human resource, structure and processes, care for community and virtuous organization. Structural equation modeling is employed to investigate the effects of each variable on other components. The data used in this study consists of questionnaire responses from employees in Payam e Noor University in Yazd province. A total of 250 questionnaires were sent out and a total of 211 valid responses were received. Our results have revealed that all the five variables have positive and significant impacts on virtuous organization. Among the five variables, organizational culture has the most direct impact (0.80 and human resource has the most total impact (0.844 on virtuous organization.

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.

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...

Structural complexities in the active layers of organic electronics.

Science.gov (United States)

Lee, Stephanie S; Loo, Yueh-Lin

2010-01-01

The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

Organic bulk heterojunction photovoltaic structures: design, morphology and properties

International Nuclear Information System (INIS)

Bulavko, G V; Ishchenko, A A

2014-01-01

Main approaches to the design of organic bulk heterojunction photovoltaic structures are generalized and systematized. Novel photovoltaic materials based on fullerenes, organic dyes and related compounds, graphene, conjugated polymers and dendrimers are considered. The emphasis is placed on correlations between the chemical structure and properties of materials. The effect of morphology of the photoactive layer on the photovoltaic properties of devices is analyzed. Main methods of optimization of the photovoltaic properties are outlined. The bibliography includes 338 references

E-learning and the Educational Organizations Structure Reengineering (EOSR

Directory of Open Access Journals (Sweden)

Osama Alshara

2007-06-01

Full Text Available There are many calls for innovative learning methods that utilize advanced technologies. However, we will raise fundamental questions that look deep into the future of the educational organization. Can the educational institute survive without adapting learning technologies? Would the educational institute succeed in adapting new learning technologies without changing its organizational structure and processes? We claim that the answer to both questions is no. Our research will present the need for edu-cational institutes to incorporate learning technologies and focuses on the demand for the educational organization structure reengineering as a basic requirement for the suc-cess of incorporating learning technologies. Our study ex-plores the faculty requirements and policies and procedures of educational institutes in the UAE.The paper concludes with some discussions on findings from a case study of the need of educational organization struc-ture reengineering as a basic requirement for incorporating learning technologies.

Structural Capability of an Organization toward Innovation Capability

DEFF Research Database (Denmark)

Nielsen, Susanne Balslev; Momeni, Mostafa

2016-01-01

The scholars in the field of strategic management have developed two major approaches for attainment of competitive advantage: an approach based on environmental opportunities, and another one based on internal capabilities of an organization. Some investigations in the last two decades have...... indicated that the advantages relying on the internal capabilities of organizations may determine the competitive position of organizations better than environmental opportunities do. Characteristics of firms shows that one of the most internal capabilities that lead the organizations to the strongest...... competitive advantage in the organizations is the innovation capability. The innovation capability is associated with other organizational capabilities, and many organizations have focused on the need to identify innovation capabilities.This research focuses on recognition of the structural aspect...

STRUCTURAL ORGANIZATION OF BACTERIAL UREASES

Directory of Open Access Journals (Sweden)

Lisnyak YuV

2016-09-01

Full Text Available This brief review concerns the basic principles of structural organization of multi-subunit bacterial ureases and formation of their quaternary structure. Urease is a nickel-containing enzyme (urea amidohydrolase, ЕС 3.5.1.5 that catalyses the hydrolysis of urea to get ammonia and carbamate which then decomposes with water to get ammonia and carbon dioxide. Urease is produced by bacteria, fungi, yeast and plants. On the basis of similarities in amino acid sequences, ureases assumed to have a similar structure and conservative catalytic mechanism. Within past two decades bacterial ureases have gained much attention in research field as a virulence factor in human and animal infections. The first crystal structure of urease has been determined for that from Klebsiella aerogenes. The native enzyme consists of three subunits, UreA (α-chain, UreB (β-chain and UreC (γ-chain, and contains four structural domains: two in α-chain (α-domain 1 and α-domain-2, one in β- and one in γ-chain. These three chains form a T-shaped heterotrimer αβγ. Three αβγ heterotrimers form quaternary complex (αβγ3. In case of Helicobacter pilori, the analogous trimers of corresponding dimeric subunits (αβ3 form tetrameric structure ((αβ34 in which four trimers are situated at the vertexes of the regular triangle pyramid. Active center is located in α-domain 1 and contains two atoms of nickel coordinated by residues His134, His136, carboxylated Lys217, His 246, His272 and Asp360, as well as residues involved in binding (His219 and catalysis (His320. Active site is capped by a flap that controls substrate ingress to and product egress from the dinickel center. Urease requires accessory proteins (UreD, UreF, UreG and UreE for the correct assembly of their Ni-containing metallocenters. The accessory proteins UreD, UreF, and UreG sequentially bind to the apoprotein (UreABC3 to finally form (UreABC-UreDFG3 activation complex. UreE metallochaperone delivers

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.

Developmental changes in organization of structural brain networks.

Science.gov (United States)

Khundrakpam, Budhachandra S; Reid, Andrew; Brauer, Jens; Carbonell, Felix; Lewis, John; Ameis, Stephanie; Karama, Sherif; Lee, Junki; Chen, Zhang; Das, Samir; Evans, Alan C

2013-09-01

Recent findings from developmental neuroimaging studies suggest that the enhancement of cognitive processes during development may be the result of a fine-tuning of the structural and functional organization of brain with maturation. However, the details regarding the developmental trajectory of large-scale structural brain networks are not yet understood. Here, we used graph theory to examine developmental changes in the organization of structural brain networks in 203 normally growing children and adolescents. Structural brain networks were constructed using interregional correlations in cortical thickness for 4 age groups (early childhood: 4.8-8.4 year; late childhood: 8.5-11.3 year; early adolescence: 11.4-14.7 year; late adolescence: 14.8-18.3 year). Late childhood showed prominent changes in topological properties, specifically a significant reduction in local efficiency, modularity, and increased global efficiency, suggesting a shift of topological organization toward a more random configuration. An increase in number and span of distribution of connector hubs was found in this age group. Finally, inter-regional connectivity analysis and graph-theoretic measures indicated early maturation of primary sensorimotor regions and protracted development of higher order association and paralimbic regions. Our finding reveals a time window of plasticity occurring during late childhood which may accommodate crucial changes during puberty and the new developmental tasks that an adolescent faces.

The psichological peculiarity structure organization of pupils and students

OpenAIRE

N P Kirina

2009-01-01

The article considers age differences of the psychological structure of pupils and students organization baseol on the general-functional approach to studying the qualities of the personality, which gives an opportunity to study age pecularities of organization in detail.

Growth and characterization of para-hexaphenyl based organic hetero-structures

International Nuclear Information System (INIS)

Schwabegger, G.

2013-01-01

The properties of organic semiconductors have been studied intensively in the last two decades. The main motivation for these research efforts are possible applications of this material class as building blocks of organic light emitting diodes (OLEDs) and organic field effect transistors (OFETs). Additionally, there is considerable interest concerning the optical properties of this material class including strong fluorescence and a high absorption cross section for stimulated emission. Consequently, it seems to be promising to utilize such molecules for organic solid state lasers. A profound understanding of the crystallization processes of organic semiconductor materials is necessary in order to realize such applications. The latter statement motivates the main focus of this work, which is the preparation and characterization of crystalline organic nanostructures consisting of oligomer molecules vacuum deposited on inorganic substrates by means of hot wall epitaxy (HWE). With this respect, the molecule para-Hexaphenyl (6P) and the substrate muscovite mica have achieved outstanding importance, because this combination leads to the formation of crystalline and highly anisotropic nano-needles. These nano-needles exhibit intense polarized fluorescence in the blue spectral regime and they can be utilized as wave-guides and as sources for laser radiation. To enlarge the spectrum of conceivable applications and to change the emission properties of the nano-structures, 6P can be replaced by other organic molecules. However this usually leads to multiple (non-parallel) needle orientations causing crossing points, which is cumbersome for the proposed optical applications. Organic-organic multilayer systems are discussed in this work as a possible strategy to overcome these limitations, which combines the outstanding structural properties of 6P with different optical properties of molecules like sexithiophene (6T). The morphology and structure of such multilayer organic

Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces.

Science.gov (United States)

Pagaling, E; Yang, K; Yan, T

2014-07-01

To investigate the acidophilic bacterial communities involved in microbially induced concrete corrosion (MICC). Our study sites located downstream from a forced main provided a unique opportunity to study the microbial communities involved in MICC under different environmental conditions (gradients of atmospheric H(2)S, sulphate concentration and pH) and under pipe modifications (coated vs uncoated). Bacterial cell density estimated by both cultivation- and DNA-based methods was low in the corroded sewer samples. Pyrosequencing and cloning showed that Mycobacterium and Acidithiobacillus dominated the acidophilic microbial communities. Methylacidiphilum was also dominant in samples where methane was detected. Correlation analysis indicated that Mycobacterium and Acidithiobacillus were significantly affected by pH and that Mycobacterium could better withstand highly acidic conditions compared to Acidithiobacillus. Communities dominated by Mycobacterium favoured conditions in the lined sewer pipes, while communities with a higher relative abundance of Acidithiobacillus favoured the unlined sewer pipes. Identifying the key micro-organisms involved in MICC and knowing how they interact with their environment are essential aspects for identifying steps towards concrete corrosion management. © 2014 The Society for Applied Microbiology.

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

Directory of Open Access Journals (Sweden)

Edward Alain B. Pajarillo

2015-04-01

Full Text Available This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level. Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

KAUST Repository

Qian, Peiyuan

2010-07-29

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

KAUST Repository

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

2010-01-01

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

Insights into the Regulation of Rhizosphere Bacterial Communities by Application of Bio-organic Fertilizer in Pseudostellaria heterophylla Monoculture Regime

Directory of Open Access Journals (Sweden)

Linkun Wu

2016-11-01

Full Text Available The biomass and quality of Pseudostellariae heterophylla suffers a significant decline under monoculture. Since rhizosphere microbiome plays crucial roles in soil health, deep pyrosequencing combined with qPCR was applied to characterize the composition and structure of soil bacterial community under monoculture and different amendments. The results showed compared with the first-year planted (FP, second-year monoculture of P. heterophylla (SP led to a significant decline in yield and resulted in a significant increase in Fusarium oxysporum but a decline in Burkholderia spp. Bio-organic fertilizer (MT formulated by combining antagonistic bacteria with organic matter could significantly promote the yield by regulating rhizosphere bacterial community. However, organic fertilizer (MO without antagonistic bacteria could not suppress Fusarium wilt. Multivariate statistics analysis showed a distinct separation between the healthy samples (FP and MT and the unhealthy samples (SP and MO, suggesting a strong relationship between soil microbial community and plant performance. Furthermore, we found the application of bio-organic fertilizer MT could significantly increase the bacterial community diversity and restructure microbial community with relatively fewer pathogenic F. oxysporum and more beneficial Burkholderia spp. In conclusion, the application of novel bio-organic fertilizer could effectively suppress Fusarium wilt by enriching the antagonistic bacteria and enhancing the bacterial diversity.

Chiral Organic Cages with a Triple-Stranded Helical Structure Derived from Helicene.

Science.gov (United States)

Malik, Abaid Ullah; Gan, Fuwei; Shen, Chengshuo; Yu, Na; Wang, Ruibin; Crassous, Jeanne; Shu, Mouhai; Qiu, Huibin

2018-02-28

We report the use of helicene with an intrinsic helical molecular structure to prepare covalent organic cages via imine condensation. The organic cages revealed a [3+2]-type architecture containing a triple-stranded helical structure with three helicene units arranged in a propeller-like fashion with the framework integrally twisted. Such structural chirality was retained upon dissolution in organic solvents, as indicated by a strong diastereotopy effect in proton NMR and unique Cotton effects in circular dichroism spectra. Further study on chiral adsorption showed that the chiral organic cages possess considerable enantioselectivity toward a series of aromatic racemates.

Assembly, Structure, and Functionality of Metal-Organic Networks and Organic Semiconductor Layers at Surfaces

Science.gov (United States)

Tempas, Christopher D.

Self-assembled nanostructures at surfaces show promise for the development of next generation technologies including organic electronic devices and heterogeneous catalysis. In many cases, the functionality of these nanostructures is not well understood. This thesis presents strategies for the structural design of new on-surface metal-organic networks and probes their chemical reactivity. It is shown that creating uniform metal sites greatly increases selectivity when compared to ligand-free metal islands. When O2 reacts with single-site vanadium centers, in redox-active self-assembled coordination networks on the Au(100) surface, it forms one product. When O2 reacts with vanadium metal islands on the same surface, multiple products are formed. Other metal-organic networks described in this thesis include a mixed valence network containing Pt0 and PtII and a network where two Fe centers reside in close proximity. This structure is stable to temperatures >450 °C. These new on-surface assemblies may offer the ability to perform reactions of increasing complexity as future heterogeneous catalysts. The functionalization of organic semiconductor molecules is also shown. When a few molecular layers are grown on the surface, it is seen that the addition of functional groups changes both the film's structure and charge transport properties. This is due to changes in both first layer packing structure and the pi-electron distribution in the functionalized molecules compared to the original molecule. The systems described in this thesis were studied using high-resolution scanning tunneling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy. Overall, this work provides strategies for the creation of new, well-defined on-surface nanostructures and adds additional chemical insight into their properties.

Non-classical structures of organic compounds: unusual stereochemistry and hypercoordination

International Nuclear Information System (INIS)

Minkin, Vladimir I; Minyaev, Ruslan M; Hoffmann, Roald

2002-01-01

Non-classical structures of organic compounds are defined as molecules containing non-tetrahedral tetracoordinate and/or hypercoordinate carbon atoms. The evolution of the views on this subject is considered and the accumulated theoretical and experimental data on the structures and dynamic transformations of non-classical organic compounds are systematised. It is shown that computational analysis using the methods and the software potential of modern quantum chemistry has now acquired high predictive capacity and is the most important source of data on the structures of non-classical compounds. The bibliography includes 227 references.

Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water

Science.gov (United States)

Islam, M. Shahinoor; Zhang, Yanyan; McPhedran, Kerry N.

2015-01-01

The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>109 gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

Science.gov (United States)

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

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Daochen Zhu

Full Text Available BACKGROUND: Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS: Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. CONCLUSIONS: This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Organizations in America: Analyzing Their Structures and Human Resource Practices Based on the National Organizations Study.

Science.gov (United States)

Kalleberg, Arne L.; Knoke, David; Marsden, Peter V.; Spaeth, Joe L.

In 1991 the National Organizations Study (NOS) surveyed a number of U.S. businesses about their structure, context, and personnel practices to produce a database for answering questions about social behavior in work organizations. This book presents the results of that survey. The study aimed to create a national database on organizations--based…

Structural Genomics of Minimal Organisms: Pipeline and Results

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-Hou; Shin, Dong-Hae; Kim, Rosalind; Adams, Paul; Chandonia, John-Marc

2007-09-14

The initial objective of the Berkeley Structural Genomics Center was to obtain a near complete three-dimensional (3D) structural information of all soluble proteins of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter has fewer than 700 genes. A semiautomated structural genomics pipeline was set up from target selection, cloning, expression, purification, and ultimately structural determination. At the time of this writing, structural information of more than 93percent of all soluble proteins of M. genitalium is avail able. This chapter summarizes the approaches taken by the authors' center.

Integrating centralized and decentralized organization structures: an education and development model.

Science.gov (United States)

Sheriff, R; Banks, A

2001-01-01

Organization change efforts have led to critically examining the structure of education and development departments within hospitals. This qualitative study evaluated an education and development model in an academic health sciences center. The model combines centralization and decentralization. The study results can be used by staff development educators and administrators when organization structure is questioned. This particular model maximizes the benefits and minimizes the limitations of centralized and decentralized structures.

The environmental structure to the interior of the organization

International Nuclear Information System (INIS)

Angel Sanint, Enrique

1998-01-01

The tasks to perform by any area are presented for the two basic types of environmental structure within the organization, function oriented and process oriented - based on that classification, advantages and disadvantages are identified for both structures. Finally, some additional coordination mechanisms are proposed in order to make the process oriented structure more flexible

cDNA structure, genomic organization and expression patterns of ...

African Journals Online (AJOL)

Visfatin was a newly identified adipocytokine, which was involved in various physiologic and pathologic processes of organisms. The cDNA structure, genomic organization and expression patterns of silver Prussian carp visfatin were described in this report. The silver Prussian carp visfatin cDNA cloned from the liver was ...

Low-Dimensional Organic Tin Bromide Perovskites and Their Photoinduced Structural Transformation.

Science.gov (United States)

Zhou, Chenkun; Tian, Yu; Wang, Mingchao; Rose, Alyssa; Besara, Tiglet; Doyle, Nicholas K; Yuan, Zhao; Wang, Jamie C; Clark, Ronald; Hu, Yanyan; Siegrist, Theo; Lin, Shangchao; Ma, Biwu

2017-07-24

Hybrid organic-inorganic metal halide perovskites possess exceptional structural tunability, with three- (3D), two- (2D), one- (1D), and zero-dimensional (0D) structures on the molecular level all possible. While remarkable progress has been realized in perovskite research in recent years, the focus has been mainly on 3D and 2D structures, with 1D and 0D structures significantly underexplored. The synthesis and characterization of a series of low-dimensional organic tin bromide perovskites with 1D and 0D structures is reported. Using the same organic and inorganic components, but at different ratios and reaction conditions, both 1D (C 4 N 2 H 14 )SnBr 4 and 0D (C 4 N 2 H 14 Br) 4 SnBr 6 can be prepared in high yields. Moreover, photoinduced structural transformation from 1D to 0D was investigated experimentally and theoretically in which photodissociation of 1D metal halide chains followed by structural reorganization leads to the formation of a more thermodynamically stable 0D structure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

Science.gov (United States)

Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

2014-03-01

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

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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.

Metal-organic frameworks: structure, properties, methods of synthesis and characterization

International Nuclear Information System (INIS)

Butova, V V; Soldatov, M A; Guda, A A; Lomachenko, K A; Lamberti, C

2016-01-01

This review deals with key methods of synthesis and characterization of metal-organic frameworks (MOFs). The modular structure affords a wide variety of MOFs with different active metal sites and organic linkers. These compounds represent a new stage of development of porous materials in which the pore size and the active site structure can be modified within wide limits. The set of experimental methods considered in this review is sufficient for studying the short-range and long-range order of the MOF crystal structure, determining the morphology of samples and elucidating the processes that occur at the active metal site in the course of chemical reactions. The interest in metal-organic frameworks results, first of all, from their numerous possible applications, ranging from gas separation and storage to chemical reactions within the pores. The bibliography includes 362 references

Using the Cambridge structure database of organic and organometalic compounds in structure biology

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich

2010-01-01

Roč. 17, 1a (2010), b24-b26 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. Nové Hrady, 18.03.2010-20.03.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : organic chemistry * Cambridge Structure Data base * molecular structure Subject RIV: CD - Macromolecular Chemistry http://xray.cz/ms/bul2010-1a/friday2.pdf

Resensi Buku: Organization Strategy, Structure, and Process

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Ayi Ahadiyat

2009-08-01

Full Text Available Book ReviewJudul Buku    : Organization Strategy, Structure, and ProcessPenulis    : Raymond E. Miles and Charles C. SnowPenerbit     : McGraw-Hill Kogakusha, Ltd (International Student Edition, Tokyo,  274 hlm.Tahun    : 1978

Two-plane symmetry in the structural organization of man.

Science.gov (United States)

Ermolenko, A E

2005-01-01

Manifestations of symmetry in the human structural organization in ontogenesis and phylogenetic development are analysed. A concept of macrobiocrystalloid with inherent complex symmetry is proposed for the description of the human organism in its integrity. The symmetry can be characterized as two-plane radial (quadrilateral), where the planar symmetry is predominant while the layout of organs of radial symmetry is subordinated to it. Out of the two planes of symmetry (sagittal and horizontal), the sagittal plane is predominant: (a) the location of the organs is governed by two principles: in compliance with the symmetry planes and in compliance with the radial symmetry around cavities; (b) the location of the radial symmetry organs is also governed by the principle of two-plane symmetry; (c) out of the four antimeres of two-plane symmetry, two are paired while the other two have merged into one organ; (d) some organs which are antimeres relative to the horizontal plane are located at the cranial end of the organism (sensory organs, cerebrum-cerebellum, heart-spleen and others). The two-plane symmetry is formed by two mechanisms--(a) the impact of morphogenetic fields of the whole crystalloid organism during embriogenesis and (b) genetic mechanisms of the development of chromosomes having two-plane symmetry. When comparing mineral and biological entities we should consider not the whole immobile crystal but only the active superficial part of a growing or dissolving crystal, the interface between the crystal surface and the crystal-forming environment which directly controls crystal growth and adapts itself to it, as well as crystal feed stock expressed in the structure of concentration flows. The symmetry of the chromosome, of the embrion at the early stages of cell cleavage as well as of some organs and systems in their phylogenetic development is described.

Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra

Science.gov (United States)

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species. PMID:22837688

Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra.

Science.gov (United States)

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1-10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni's correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.

Discerning Thermodynamic Basis of Self-Organization in Critical Zone Structure and Function

Science.gov (United States)

Richardson, M.; Kumar, P.

2017-12-01

Self-organization characterizes the spontaneous emergence of order. Self-organization in the Critical Zone, the region of Earth's skin from below the groundwater table to the top of the vegetation canopy, involves the interaction of biotic and abiotic processes occurring through a hierarchy of temporal and spatial scales. The self-organization is sustained through input of energy and material in an open system framework, and the resulting formations are called dissipative structures. Why do these local states of organization form and how are they thermodynamically favorable? We hypothesize that structure formation is linked to energy conversion and matter throughput rates across driving gradients. Furthermore, we predict that structures in the Critical Zone evolve based on local availability of nutrients, water, and energy. By considering ecosystems as open thermodynamic systems, we model and study the throughput signatures on short times scales to determine origins and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of matter and energy to understand the thermodynamic drivers of the system. By classifying the fluxes and dynamics in a system, we can identify patterns to determine the thermodynamic drivers for organized states. Additionally, studying the partitioning of nutrients, water, and energy throughout ecosystems through dissipative structures will help identify reasons for structure shapes and how these shapes impact major Critical Zone functions.

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.

Stability of material in dynamics of structural organization

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Vyrovoy Valery

2017-01-01

Full Text Available Formation of the scientific ideology is based on the basic model of the structured medium and demands the formalization of the term «structure». The objects-systems are offered to be present in the form of models. It is shown that the mechanism of structure formation on the solid level where gravity prevails differs from mechanism of structure formation at the level where forces of interparticle interactions dominate. It is asserted that geometrical characteristics of products define conditions of the organization of its integral structure. Rather independent coexistence of various solid levels assumes spontaneous realization of various interconnected events which provides the wholeness and safe functioning of a construction-system.

Persistence of urban organic aerosols composition: Decoding their structural complexity and seasonal variability

International Nuclear Information System (INIS)

Matos, João T.V.; Duarte, Regina M.B.O.; Lopes, Sónia P.; Silva, Artur M.S.; Duarte, Armando C.

2017-01-01

Organic Aerosols (OAs) are typically defined as highly complex matrices whose composition changes in time and space. Focusing on time vector, this work uses two-dimensional nuclear magnetic resonance (2D NMR) techniques to examine the structural features of water-soluble (WSOM) and alkaline-soluble organic matter (ASOM) sequentially extracted from fine atmospheric aerosols collected in an urban setting during cold and warm seasons. This study reveals molecular signatures not previously decoded in NMR-related studies of OAs as meaningful source markers. Although the ASOM is less hydrophilic and structurally diverse than its WSOM counterpart, both fractions feature a core with heteroatom-rich branched aliphatics from both primary (natural and anthropogenic) and secondary origin, aromatic secondary organics originated from anthropogenic aromatic precursors, as well as primary saccharides and amino sugar derivatives from biogenic emissions. These common structures represent those 2D NMR spectral signatures that are present in both seasons and can thus be seen as an “annual background” profile of the structural composition of OAs at the urban location. Lignin-derived structures, nitroaromatics, disaccharides, and anhydrosaccharides signatures were also identified in the WSOM samples only from periods identified as smoke impacted, which reflects the influence of biomass-burning sources. The NMR dataset on the H–C molecules backbone was also used to propose a semi-quantitative structural model of urban WSOM, which will aid efforts for more realistic studies relating the chemical properties of OAs with their atmospheric behavior. - Highlights: • 2D NMR spectroscopy was used to decode urban organic aerosols. • Water and alkaline soluble components of urban organic aerosols have been compared. • Persistence of urban organic aerosols composition across different seasons. • Annual background profile of the structural features of urban organic aerosols. • Semi

The role of the organization structure in the diffusion of innovations.

Science.gov (United States)

Sáenz-Royo, Carlos; Gracia-Lázaro, Carlos; Moreno, Yamir

2015-01-01

Diffusion and adoption of innovations is a topic of increasing interest in economics, market research, and sociology. In this paper we investigate, through an agent based model, the dynamics of adoption of innovative proposals in different kinds of structures. We show that community structure plays an important role on the innovation diffusion, so that proposals are more likely to be accepted in homogeneous organizations. In addition, we show that the learning process of innovative technologies enhances their diffusion, thus resulting in an important ingredient when heterogeneous networks are considered. We also show that social pressure blocks the adoption process whatever the structure of the organization. These results may help to understand how different factors influence the diffusion and acceptance of innovative proposals in different communities and organizations.

Family Structure as a Correlate of Organized Sport Participation among Youth.

Science.gov (United States)

McMillan, Rachel; McIsaac, Michael; Janssen, Ian

2016-01-01

Organized sport is one way that youth participate in physical activity. There are disparities in organized sport participation by family-related factors. The purpose of this study was to determine whether non-traditional family structure and physical custody arrangements are associated with organized sport participation in youth, and if so whether this relationship is mediated by socioeconomic status. Data were from the 2009-10 Health Behaviour in School-aged Children survey, a nationally representative cross-section of Canadian youth in grades 6-10 (N = 21,201). Information on family structure was derived from three survey items that asked participants the number of adults they lived with, their relationship to these adults, and if applicable, how often they visited another parent outside their home. Participants were asked whether or not they were currently involved in an organized sport. Logistic regression was used to compare the odds of organized sport participation according to family structure. Bootstrap-based mediation analysis was used to assess mediation by perceived family wealth. The results indicated that by comparison to traditional families, boys and girls from reconstituted families with irregular visitation of a second parent, reconstituted families with regular visitation of a second parent, single-parent families with irregular visitation of a second parent, and single-parent families with regular visitation of a second parent were less likely to participate in organized sport than those from traditional families, with odds ratios ranging from 0.48 (95% confidence interval: 0.38-0.61) to 0.78 (95% confidence interval: 0.56-1.08). The relationship between family structure and organized sport was significantly mediated by perceived family wealth, although the magnitude of the mediation was modest (ie, reconstituted families experienced significant disparities in organized sport participation that was partially mediated by perceived family wealth.

Interfacial self-organization of bolaamphiphiles bearing mesogenic groups: relationships between the molecular structures and their self-organized morphologies.

Science.gov (United States)

Song, Bo; Liu, Guanqing; Xu, Rui; Yin, Shouchun; Wang, Zhiqiang; Zhang, Xi

2008-04-15

This article discusses the relationship between the molecular structure of bolaamphiphiles bearing mesogenic groups and their interfacial self-organized morphology. On the basis of the molecular structures of bolaamphiphiles, we designed and synthesized a series of molecules with different hydrophobic alkyl chain lengths, hydrophilic headgroups, mesogenic groups, and connectors between the alkyl chains and the mesogenic group. Through investigating their interfacial self-organization behavior, some experiential rules are summarized: (1) An appropriate alkyl chain length is necessary to form stable surface micelles; (2) different categories of headgroups have a great effect on the interfacial self-organized morphology; (3) different types of mesogenic groups have little effect on the structure of the interfacial assembly when it is changed from biphenyl to azobenzene or stilbene; (4) the orientation of the ester linker between the mesogenic group and alkyl chain can greatly influence the interfacial self-organization behavior. It is anticipated that this line of research may be helpful for the molecular engineering of bolaamphiphiles to form tailor-made morphologies.

Near-unity mass accommodation coefficient of organic molecules of varying structure.

Science.gov (United States)

Julin, Jan; Winkler, Paul M; Donahue, Neil M; Wagner, Paul E; Riipinen, Ilona

2014-10-21

Atmospheric aerosol particles have a significant effect on global climate, air quality, and consequently human health. Condensation of organic vapors is a key process in the growth of nanometer-sized particles to climate relevant sizes. This growth is very sensitive to the mass accommodation coefficient α, a quantity describing the vapor uptake ability of the particles, but knowledge on α of atmospheric organics is lacking. In this work, we have determined α for four organic molecules with diverse structural properties: adipic acid, succinic acid, naphthalene, and nonane. The coefficients are studied using molecular dynamics simulations, complemented with expansion chamber measurements. Our results are consistent with α = 1 (indicating nearly perfect accommodation), regardless of the molecular structural properties, the phase state of the bulk condensed phase, or surface curvature. The results highlight the need for experimental techniques capable of resolving the internal structure of nanoparticles to better constrain the accommodation of atmospheric organics.

Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water.

Science.gov (United States)

Islam, M Shahinoor; Zhang, Yanyan; McPhedran, Kerry N; Liu, Yang; Gamal El-Din, Mohamed

2015-06-15

The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Consumer knowledge structures with regards to organic foods

DEFF Research Database (Denmark)

Bredahl, Lone; Thøgersen, John; Dean, Moira

2004-01-01

associated with self-relevant consequences do not appear to discriminate clearly among segments, however. Generally, organic origin has significant links to personal values among segments of adventurous, enthusiastic, hedonistic and eco-healthy food consumers while it appears a dysfunctional means......This paper presents results of an empirical study conducted among European consumers to explore consumer knowledge structures with regard to organic foods and to identify the beliefs and the attribute-to-value chains that discriminate best among different consumer segments. Using means-end chain...... theory as the theoretical basis, the objectives of the study were met through carrying out laddering interviews with consumers in Germany, Great Britain, Denmark and Spain, using a Food-Related Lifestyle (FRL) segment-based approach and interviewing both organic and non-organic consumers. Respondents...

Pyrosequencing reveals bacterial communities in unchlorinated drinking water distribution system: an integral study of bulk water, suspended solids, loose deposits, and pipe wall biofilm.

Science.gov (United States)

Liu, G; Bakker, G L; Li, S; Vreeburg, J H G; Verberk, J Q J C; Medema, G J; Liu, W T; Van Dijk, J C

2014-05-20

The current understanding of drinking water distribution system (DWDS) microbiology is limited to pipe wall biofilm and bulk water; the contributions of particle-associated bacteria (from suspended solids and loose deposits) have long been neglected. Analyzing the composition and correlation of bacterial communities from different phases helped us to locate where most of the bacteria are and understand the interactions among these phases. In the present study, the bacteria from four critical phases of an unchlorinated DWDS, including bulk water, pipe wall biofilm, suspended solids, and loose deposits, were quantified and identified by adenosine triphosphate analysis and pyrosequencing, respectively. The results showed that the bulk water bacteria (including the contribution of suspended solids) contributed less than 2% of the total bacteria. The bacteria associated with loose deposits and pipe wall biofilm that accumulated in the DWDS accounted for over 98% of the total bacteria, and the contributions of bacteria in loose deposits and pipe wall biofilm were comparable. Depending on the amount of loose deposits, its contribution can be 7-fold higher than the pipe wall biofilm. Pyrosequencing revealed relatively stable bacterial communities in bulk water, pipe wall biofilm, and suspended solids throughout the distribution system; however, the communities present in loose deposits were dependent on the amount of loose deposits locally. Bacteria within the phases of suspended solids, loose deposits, and pipe wall biofilm were similar in phylogenetic composition. The bulk water bacteria (dominated by Polaromonas spp.) were clearly different from the bacteria from the other three phases (dominated by Sphingomonas spp.). This study highlighted that the integral DWDS ecology should include contributions from all of the four phases, especially the bacteria harbored by loose deposits. The accumulation of loose deposits and the aging process create variable microenvironments

Pyrosequencing Reveals Bacterial Communities in Unchlorinated Drinking Water Distribution System: An Integral Study of Bulk Water, Suspended Solids, Loose Deposits, and Pipe Wall Biofilm

KAUST Repository

Liu, G.

2014-05-20

The current understanding of drinking water distribution system (DWDS) microbiology is limited to pipe wall biofilm and bulk water; the contributions of particle-associated bacteria (from suspended solids and loose deposits) have long been neglected. Analyzing the composition and correlation of bacterial communities from different phases helped us to locate where most of the bacteria are and understand the interactions among these phases. In the present study, the bacteria from four critical phases of an unchlorinated DWDS, including bulk water, pipe wall biofilm, suspended solids, and loose deposits, were quantified and identified by adenosine triphosphate analysis and pyrosequencing, respectively. The results showed that the bulk water bacteria (including the contribution of suspended solids) contributed less than 2% of the total bacteria. The bacteria associated with loose deposits and pipe wall biofilm that accumulated in the DWDS accounted for over 98% of the total bacteria, and the contributions of bacteria in loose deposits and pipe wall biofilm were comparable. Depending on the amount of loose deposits, its contribution can be 7-fold higher than the pipe wall biofilm. Pyrosequencing revealed relatively stable bacterial communities in bulk water, pipe wall biofilm, and suspended solids throughout the distribution system; however, the communities present in loose deposits were dependent on the amount of loose deposits locally. Bacteria within the phases of suspended solids, loose deposits, and pipe wall biofilm were similar in phylogenetic composition. The bulk water bacteria (dominated by Polaromonas spp.) were clearly different from the bacteria from the other three phases (dominated by Sphingomonas spp.). This study highlighted that the integral DWDS ecology should include contributions from all of the four phases, especially the bacteria harbored by loose deposits. The accumulation of loose deposits and the aging process create variable microenvironments

Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

Science.gov (United States)

Yabuzaki, Junko

2017-01-01

To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp. © The Author(s) 2017. Published by Oxford University Press.

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.

Advanced organic and biological analysis of dual media filtration used as a pretreatment in a full-scale seawater desalination plant

KAUST Repository

Jeong, Sanghyun

2016-02-19

Dual media filter (DMF) is being used as a primary pretreatment to remove particulate foulants at seawater desalination plants. However, many plants experience organic and biological fouling. The first part of this paper focuses on the monitoring of organic and biological foulants using advanced analytical techniques to optimize functioning of DMF at Perth Seawater Desalination Plant (PSDP) in Western Australia. In addition, microbial community analysis in DMF filtered seawater, and on DMF media (DMF-M) and cartridge filter (CF) was conducted using terminal restriction fragment length polymorphism (T-RFLP) and 454-pyrosequencing. In the full-scale DMF system, the bacterial community structure was clustered along with the filtration time and sampling positions. For the DMF effluent samples, the bacterial community structure significantly shifted after 4 h of filtration time, which corresponded with the permeability reduction trend. The dominant bacterial communities in the DMF effluent were OTU 13 (Phaeobacter) and OTU 19 (Oceaniserpentilla). The different biofilm-forming bacteria communities were found in the biofilm samples on DMF-M and CF. In the second part of the study, semi-pilot scale DMF columns were operated on-site under same operating conditions used in PSDP. It demonstrated the advantage of operating DMF at the biofiltration mode for improving the reduction of biofoulants. © 2016 Elsevier B.V.

Advanced organic and biological analysis of dual media filtration used as a pretreatment in a full-scale seawater desalination plant

KAUST Repository

Jeong, Sanghyun; Vollprecht, Robert; Cho, Kyungjin; Leiknes, TorOve; Vigneswaran, Saravanamuthu; Bae, Hyokwan; Lee, Seockheon

2016-01-01

Dual media filter (DMF) is being used as a primary pretreatment to remove particulate foulants at seawater desalination plants. However, many plants experience organic and biological fouling. The first part of this paper focuses on the monitoring of organic and biological foulants using advanced analytical techniques to optimize functioning of DMF at Perth Seawater Desalination Plant (PSDP) in Western Australia. In addition, microbial community analysis in DMF filtered seawater, and on DMF media (DMF-M) and cartridge filter (CF) was conducted using terminal restriction fragment length polymorphism (T-RFLP) and 454-pyrosequencing. In the full-scale DMF system, the bacterial community structure was clustered along with the filtration time and sampling positions. For the DMF effluent samples, the bacterial community structure significantly shifted after 4 h of filtration time, which corresponded with the permeability reduction trend. The dominant bacterial communities in the DMF effluent were OTU 13 (Phaeobacter) and OTU 19 (Oceaniserpentilla). The different biofilm-forming bacteria communities were found in the biofilm samples on DMF-M and CF. In the second part of the study, semi-pilot scale DMF columns were operated on-site under same operating conditions used in PSDP. It demonstrated the advantage of operating DMF at the biofiltration mode for improving the reduction of biofoulants. © 2016 Elsevier B.V.

The Influence of Content Organization on Student's Cognitive Structure in Thermodynamics.

Science.gov (United States)

Moreira, Marco A.; Santos, Carlos A.

1981-01-01

Two approaches to the content of thermodynamics were used in an introductory college physics course: traditional organization and organization based on Ausubel's learning theory. The influence of these organizations on engineering student's (N=58) cognitive structure was investigated using a word association test analyzed through hierarchical…

Structure of the Buried Metal-Molecule Interface in Organic Thin Film Devices

DEFF Research Database (Denmark)

Hansen, Christian Rein; Sørensen, Thomas Just; Glyvradal, Magni

2009-01-01

By use of specular X-ray reflectivity (XR) the structure of a metal-covered organic thin film device is measured with angstrom resolution. The model system is a Langmuir-Blodgett (LB) film, sandwiched between a silicon substrate and a top electrode consisting of 25 Å titanium and 100 Å aluminum....... By comparison of XR data for the five-layer Pb2+ arachidate LB film before and after vapor deposition of the Ti/Al top electrode, a detailed account of the structural damage to the organic film at the buried metal-molecule interface is obtained. We find that the organized structure of the two topmost LB layers...

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

Science.gov (United States)

Subramaniam, Karthigeyan

2016-01-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and…

Additive Manufacturing of Biomedical Constructs with Biomimetic Structural Organizations.

Science.gov (United States)

Li, Xiao; He, Jiankang; Zhang, Weijie; Jiang, Nan; Li, Dichen

2016-11-09

Additive manufacturing (AM), sometimes called three-dimensional (3D) printing, has attracted a lot of research interest and is presenting unprecedented opportunities in biomedical fields, because this technology enables the fabrication of biomedical constructs with great freedom and in high precision. An important strategy in AM of biomedical constructs is to mimic the structural organizations of natural biological organisms. This can be done by directly depositing cells and biomaterials, depositing biomaterial structures before seeding cells, or fabricating molds before casting biomaterials and cells. This review organizes the research advances of AM-based biomimetic biomedical constructs into three major directions: 3D constructs that mimic tubular and branched networks of vasculatures; 3D constructs that contains gradient interfaces between different tissues; and 3D constructs that have different cells positioned to create multicellular systems. Other recent advances are also highlighted, regarding the applications of AM for organs-on-chips, AM-based micro/nanostructures, and functional nanomaterials. Under this theme, multiple aspects of AM including imaging/characterization, material selection, design, and printing techniques are discussed. The outlook at the end of this review points out several possible research directions for the future.

Autonomy and structure can enhance motivation of volunteers in sport organizations.

Science.gov (United States)

Hsu, Wei Ting; Wu, Kou Hsien; Wang, Yi Ching; Hsiao, Chia Huei; Wu, Hui Chin

2013-12-01

The goal was better understanding of the motivational factors of volunteers in non-profit sport organizations. The roles of two factors provided by supervisors to their subordinates were examined: autonomy support, i.e., the encouragement of self-initiation and emphasis on choice rather than control, and structure, i.e., the introduction of order, definite procedures, and rules. 489 sport volunteers (289 men, 200 women; M age = 31.2 yr., SD = 7.4) were administered questionnaires assessing their perceived autonomy support, structure, and motivation. Regression analysis indicated that perceived autonomy support predicted motivation. Structure also mediated the effect of perceived autonomy support on motivation. Supervisors of sport organizations should provide adequate structure for their volunteers.

Threedimensional imaging of organ structures by nuclear magnetic resonance

International Nuclear Information System (INIS)

Waters, W.; Smolorz, J.; Wellner, U.

1985-01-01

A simple method for threedimensional imaging of organ structures is presented. The method is based on a special acquisition mode in a nuclear resonance tomograph, exciting layers of 20 cm thickness at different angulations. The display is done by cinematography (which is usually used in nuclear cardiology) projecting the structures in a rotating movement. (orig.) [de

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

Science.gov (United States)

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai

Solution processable inverted structure ZnO-organic hybrid heterojuction white LEDs

Science.gov (United States)

Bano, N.; Hussain, I.; Soomro, M. Y.; EL-Naggar, A. M.; Albassam, A. A.

2018-05-01

Improving luminance efficiency and colour purity are the most important challenges for zinc oxide (ZnO)-organic hybrid heterojunction light emitting diodes (LEDs), affecting their large area applications. If ZnO-organic hybrid heterojunction white LEDs are fabricated by a hydrothermal method, it is difficult to obtain pure and stable blue emission from PFO due to the presence of an undesirable green emission. In this paper, we present an inverted-structure ZnO-organic hybrid heterojunction LED to avoid green emission from PFO, which mainly originates during device processing. With this configuration, each ZnO nanorod (NR) forms a discrete p-n junction; therefore, large-area white LEDs can be designed without compromising the junction area. The configuration used for this novel structure is glass/ZnO NRs/PFO/PEDOT:PSS/L-ITO, which enables the development of efficient, large-area and low-cost hybrid heterojunction LEDs. Inverted-structure ZnO-organic hybrid heterojunction white LEDs offer several improvements in terms of brightness, size, colour, external quantum efficiency and a wider applicability as compared to normal architecture LEDs.

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

Directory of Open Access Journals (Sweden)

Jiang eZhu

2012-09-01

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

Family Structure as a Correlate of Organized Sport Participation among Youth.

Directory of Open Access Journals (Sweden)

Rachel McMillan

Full Text Available Organized sport is one way that youth participate in physical activity. There are disparities in organized sport participation by family-related factors. The purpose of this study was to determine whether non-traditional family structure and physical custody arrangements are associated with organized sport participation in youth, and if so whether this relationship is mediated by socioeconomic status. Data were from the 2009-10 Health Behaviour in School-aged Children survey, a nationally representative cross-section of Canadian youth in grades 6-10 (N = 21,201. Information on family structure was derived from three survey items that asked participants the number of adults they lived with, their relationship to these adults, and if applicable, how often they visited another parent outside their home. Participants were asked whether or not they were currently involved in an organized sport. Logistic regression was used to compare the odds of organized sport participation according to family structure. Bootstrap-based mediation analysis was used to assess mediation by perceived family wealth. The results indicated that by comparison to traditional families, boys and girls from reconstituted families with irregular visitation of a second parent, reconstituted families with regular visitation of a second parent, single-parent families with irregular visitation of a second parent, and single-parent families with regular visitation of a second parent were less likely to participate in organized sport than those from traditional families, with odds ratios ranging from 0.48 (95% confidence interval: 0.38-0.61 to 0.78 (95% confidence interval: 0.56-1.08. The relationship between family structure and organized sport was significantly mediated by perceived family wealth, although the magnitude of the mediation was modest (ie, <20% change in effect estimate. In conclusion, youth living in both single-parent and reconstituted families experienced significant

Structural Modification of Organic Thin-Film Transistors for Photosensor Application

Science.gov (United States)

Jeong, Hyeon Seok; Bae, Jin-Hyuk; Lee, Hyeonju; Ndikumana, Joel; Park, Jaehoon

2018-05-01

We investigated the light response characteristics of bottom-gate/top-contact organic TFTs fabricated using pentacene and polystyrene as an organic semiconductor and a polymeric insulator, respectively. The pentacene TFT with overlaps (50 μm) between the source and gate electrodes as well as between the drain and gate electrodes exhibited negligible hysteresis in its transfer characteristics upon reversal of the gate voltage sweep direction. When the TFTs were structurally modified to produce an underlap structure between the source and gate electrodes, clockwise hysteresis and a drain-current decrease were observed, which were further augmented by increasing the gate underlap (from 30 μm to 50 μm and 70 μm). Herein, these results are explained in terms of space charge formation and accumulation capacitance reduction. Importantly, we found that space charges formed under the source electrode contributed to the drain currents via light irradiation through the underlap region. Under constant bias conditions, the TFTs with gate underlap structures thus exhibited on-state drain current changes in response to light signals. In our study, an optimal photosensitivity exceeding 11 was achieved by the TFT with a 30 μm gate underlap. Consequently, we suggest that gate underlap structure modification is a viable means of implementing light responsiveness in organic TFTs.

Relationship of subseafloor microbial diversity to sediment age and organic carbon content

Science.gov (United States)

Walsh, E. A.; Kirkpatrick, J. B.; Sogin, M. L.; D'Hondt, S. L.

2013-12-01

Our tag pyrosequencing investigation of four globally distant sites reveals sediment age and total organic carbon content to be significant components in understanding subseafloor diversity. Our sampling locations include two sites from high-productivity regions (Indian Ocean and Bering Sea) and two from moderate-productivity (eastern and central equatorial Pacific Ocean). Sediment from the high-productivity sites has much higher TOC than sediment from the moderate-productivity equatorial sites. We applied a high-resolution 16S V4-V6 tag pyrosequencing approach to 24 bacterial and 17 archaeal samples, totaling 602,502 reads. We identified1,291 archaeal and 15,910 bacterial OTUs (97%) from these reads. We analyzed bacterial samples from all four sites in addition to archaeal samples from our high productivity sites. These high productivity, high TOC sites have a pronounced methane-rich sulfate-free zone at depth from which archaea have been previously considered to dominate (Biddle et al., 2006). At all four locations, microbial diversity is highest near the seafloor and drops rapidly to low but stable values with increasing sediment depth. The depth at which diversity stabilizes varies greatly from site to site, but the age at which it stabilizes is relatively constant. At all four sites, diversity reaches low stable values a few hundred thousand years after sediment deposition. The sites with high total organic carbon (high productivity sites) generally exhibit higher diversity at each sediment age than the sites with lower total organic carbon (moderate-productivity sites). Archaeal diversity is lower than bacterial diversity at every sampled depth. Biddle, J.F., Lipp, J.S., Lever, M.A., Lloyd, K.G., Sørensen, K.B., Anderson, R. et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS 103: 3846-3851.

The Effect of the Wooden Breast Myopathy on Sarcomere Structure and Organization.

Science.gov (United States)

Velleman, Sandra G; Clark, Daniel L; Tonniges, Jeffrey R

2018-03-01

The wooden breast (WB) has been classically identified by the phenotypic presence of a wood-like pectoralis major (p. major) muscle. The WB-affected p. major muscle is characterized by necrotic muscle fibers and the replacement of muscle with connective tissue, water, and fat. The objective of the current study was to determine the effect of the WB myopathy on sarcomere organization by transmission electron microscopy. Sarcomere structure and organization were examined in two broiler lines with a high incidence of WB (Lines A and B) and another broiler line without WB (Line C). Affected muscle had an increase in smaller myofibers with diameters of 20 μm or less. Sarcomere organization decreased with fiber diameter in both Lines A and B. The structure and organization of sarcomeres in Line C were similar to WB-unaffected muscle in Lines A and B. Taken together, these data demonstrate that the WB myopathy detrimentally affects sarcomere organization in a broiler line-specific manner. Disorganization of sarcomere structure will affect the function of the p. major muscle as well as meat quality.

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.

Modelling the Impact of Organization Structure and Whistle Blowers on Intra-Organizational Corruption Contagion

OpenAIRE

Nekovee, Maziar; Pinto, Jonathan

2017-01-01

We complement the rich conceptual work on organizational corruption by quantitatively modelling the spread of corruption within organizations. We systematically vary four organizational culture-related parameters, i.e., organization structure, location of bad apple, employees propensity to become corrupted (corruption probability), and number of whistle-blowers. Our simulation studies find that in organizations with flatter structures, corruption permeates the organization at a lower threshol...

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

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

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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.

Organic-Inorganic Perovskites: Structural Versatility for Functional Materials Design.

Science.gov (United States)

Saparov, Bayrammurad; Mitzi, David B

2016-04-13

Although known since the late 19th century, organic-inorganic perovskites have recently received extraordinary research community attention because of their unique physical properties, which make them promising candidates for application in photovoltaic (PV) and related optoelectronic devices. This review will explore beyond the current focus on three-dimensional (3-D) lead(II) halide perovskites, to highlight the great chemical flexibility and outstanding potential of the broader class of 3-D and lower dimensional organic-based perovskite family for electronic, optical, and energy-based applications as well as fundamental research. The concept of a multifunctional organic-inorganic hybrid, in which the organic and inorganic structural components provide intentional, unique, and hopefully synergistic features to the compound, represents an important contemporary target.

Keeping patients safe in healthcare organizations: a structuration theory of safety culture.

Science.gov (United States)

Groves, Patricia S; Meisenbach, Rebecca J; Scott-Cawiezell, Jill

2011-08-01

This paper presents a discussion of the use of structuration theory to facilitate understanding and improvement of safety culture in healthcare organizations. Patient safety in healthcare organizations is an important problem worldwide. Safety culture has been proposed as a means to keep patients safe. However, lack of appropriate theory limits understanding and improvement of safety culture. The proposed structuration theory of safety culture was based on a critique of available English-language literature, resulting in literature published from 1983 to mid-2009. CINAHL, Communication and Mass Media Complete, ABI/Inform and Google Scholar databases were searched using the following terms: nursing, safety, organizational culture and safety culture. When viewed through the lens of structuration theory, safety culture is a system involving both individual actions and organizational structures. Healthcare organization members, particularly nurses, share these values through communication and enact them in practice, (re)producing an organizational safety culture system that reciprocally constrains and enables the actions of the members in terms of patient safety. This structurational viewpoint illuminates multiple opportunities for safety culture improvement. Nurse leaders should be cognizant of competing value-based culture systems in the organization and attend to nursing agency and all forms of communication when attempting to create or strengthen a safety culture. Applying structuration theory to the concept of safety culture reveals a dynamic system of individual action and organizational structure constraining and enabling safety practice. Nurses are central to the (re)production of this safety culture system. © 2011 Blackwell Publishing Ltd.

ERC Safety and Hygiene Programs functional organization structure and mission statement

International Nuclear Information System (INIS)

Coleman, S.R.

2000-01-01

This document provides a description of the functions, structure, commitments, and goals of the Environmental Restoration Contractor Safety and Hygiene Program. The current structure of the ERC Safety and Hygiene organization is described herein

Internal structure analysis of particle-double network gels used in a gel organ replica

Science.gov (United States)

Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

2016-04-01

In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

Metal-organic extended 2D structures: Fe-PTCDA on Au(111)

International Nuclear Information System (INIS)

Alvarez, Lucia; Caillard, Renaud; MartIn-Gago, Jose A; Mendez, Javier; Pelaez, Samuel; Serena, Pedro A

2010-01-01

In this work we combine organic molecules of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) with iron atoms on an Au (111) substrate in ultra-high vacuum conditions at different temperatures. By means of scanning tunnelling microscopy (STM) we study the formation of stable 2D metal-organic structures. We show that at certain growth conditions (temperature, time and coverage) stable 'ladder-like' nanostructures are obtained. These are the result of connecting together two metal-organic chains through PTCDA molecules placed perpendicularly, as rungs of a ladder. These structures, stable up to 450 K, can be extended in a 2D layer covering the entire surface and presenting different rotation domains. STM images at both polarities show a contrast reversal between the two molecules at the unit cell. By means of density functional theory (DFT) calculations, we confirm the stability of these structures and that their molecular orbitals are placed separately at the different molecules.

Diversity, biogeography and biodegradation potential of actinobacteria in the deep-sea sediments along the Southwest Indian Ridge

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Ping Chen

2016-08-01

Full Text Available The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.

Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge

Science.gov (United States)

Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

2016-01-01

The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

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

Science.gov (United States)

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

2014-01-01

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

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

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Meng Zhang

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

Efficient light emission from inorganic and organic semiconductor hybrid structures by energy-level tuning.

Science.gov (United States)

Schlesinger, R; Bianchi, F; Blumstengel, S; Christodoulou, C; Ovsyannikov, R; Kobin, B; Moudgil, K; Barlow, S; Hecht, S; Marder, S R; Henneberger, F; Koch, N

2015-04-15

The fundamental limits of inorganic semiconductors for light emitting applications, such as holographic displays, biomedical imaging and ultrafast data processing and communication, might be overcome by hybridization with their organic counterparts, which feature enhanced frequency response and colour range. Innovative hybrid inorganic/organic structures exploit efficient electrical injection and high excitation density of inorganic semiconductors and subsequent energy transfer to the organic semiconductor, provided that the radiative emission yield is high. An inherent obstacle to that end is the unfavourable energy level offset at hybrid inorganic/organic structures, which rather facilitates charge transfer that quenches light emission. Here, we introduce a technologically relevant method to optimize the hybrid structure's energy levels, here comprising ZnO and a tailored ladder-type oligophenylene. The ZnO work function is substantially lowered with an organometallic donor monolayer, aligning the frontier levels of the inorganic and organic semiconductors. This increases the hybrid structure's radiative emission yield sevenfold, validating the relevance of our approach.

Efficient light emission from inorganic and organic semiconductor hybrid structures by energy-level tuning

Science.gov (United States)

Schlesinger, R.; Bianchi, F.; Blumstengel, S.; Christodoulou, C.; Ovsyannikov, R.; Kobin, B.; Moudgil, K.; Barlow, S.; Hecht, S.; Marder, S.R.; Henneberger, F.; Koch, N.

2015-01-01

The fundamental limits of inorganic semiconductors for light emitting applications, such as holographic displays, biomedical imaging and ultrafast data processing and communication, might be overcome by hybridization with their organic counterparts, which feature enhanced frequency response and colour range. Innovative hybrid inorganic/organic structures exploit efficient electrical injection and high excitation density of inorganic semiconductors and subsequent energy transfer to the organic semiconductor, provided that the radiative emission yield is high. An inherent obstacle to that end is the unfavourable energy level offset at hybrid inorganic/organic structures, which rather facilitates charge transfer that quenches light emission. Here, we introduce a technologically relevant method to optimize the hybrid structure's energy levels, here comprising ZnO and a tailored ladder-type oligophenylene. The ZnO work function is substantially lowered with an organometallic donor monolayer, aligning the frontier levels of the inorganic and organic semiconductors. This increases the hybrid structure's radiative emission yield sevenfold, validating the relevance of our approach. PMID:25872919

Automated torso organ segmentation from 3D CT images using structured perceptron and dual decomposition

Science.gov (United States)

Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Mori, Kensaku

2015-03-01

This paper presents a method for torso organ segmentation from abdominal CT images using structured perceptron and dual decomposition. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. This paper proposes an organ segmentation method using structured output learning. Our method utilizes a graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weights of the graphical model by structured perceptron and estimate the best organ label for a given image by dynamic programming and dual decomposition. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 4.4%. The DICE coefficients of left lung, right lung, heart, liver, spleen, pancreas, left kidney, right kidney, and gallbladder were 0.91, 0.95, 0.77, 0.81, 0.74, 0.08, 0.83, 0.84, and 0.03, respectively.

Syntheses, characterizations and crystal structures of three new organically templated or organically bonded zinc selenates

International Nuclear Information System (INIS)

Feng Meiling; Mao Jianggao; Song Junling

2004-01-01

Three new organically templated or organically bonded zinc selenates, namely, {H 2 bipy}Zn(SeO 4 ) 2 (H 2 O) 2 1 (bipy=4,4'-bipyridine), {H 2 pip}{Zn(SeO 4 ) 2 (H 2 O) 4 }·2H 2 O 2 (pip=piprazine), and Zn(SeO 4 )(phen)(H 2 O) 2 3 (phen=1,10-phenanthroline) have been synthesized by hydrothermal reactions. The structure of compound 1 features a 1D chain composed of [Zn(SeO 4 ) 2 (H 2 O) 2 ] 2- anions. Compound 2 has a 2D layer structure built from {Zn(SeO 4 ) 2 (H 2 O) 4 } 2- anions that are cross-linked by doubly protonated piperazine cations via N-H···O hydrogen bonds. The structure of compound 3 contains a 1D chain of Zn(SeO 4 )(phen)(H 2 O) 2 , such chains are further interlinked by hydrogen bonds and π···π interactions to form a layer. The different roles the templates played have also been discussed

Structures formation through self-organized accretion on cosmic strings

International Nuclear Information System (INIS)

Murdzek, R.

2009-01-01

In this paper, we shall show that the formation of structures through accretion by a cosmic string is driven by a natural feed-back mechanism: a part of the energy radiated by accretions creates a pressure on the accretion disk itself. This phenomenon leads to a nonlinear evolution of the accretion process. Thus, the formation of structures results as a consequence of a self-organized growth of the accreting central object.

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

Directory of Open Access Journals (Sweden)

Yongcui Deng

Full Text Available The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance, Actinobacteria (17.3% and Bacteroidetes (11% had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%. In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales. Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta and methanotrophs (mainly Methylocystis compared with the other two wetlands. Principal coordinate analysis (PCoA indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of

Structural Ordering of Semiconducting Polymers and Small-Molecules for Organic Electronics

Science.gov (United States)

O'Hara, Kathryn Allison

Semiconducting polymers and small-molecules can be readily incorporated into electronic devices such as organic photovoltaics (OPVs), thermoelectrics (OTEs), organic light emitting diodes (OLEDs), and organic thin film transistors (OTFTs). Organic materials offer the advantage of being processable from solution to form flexible and lightweight thin films. The molecular design, processing, and resulting thin film morphology of semiconducting polymers drastically affect the optical and electronic properties. Charge transport within films of semiconducting polymers relies on the nanoscale organization to ensure electronic coupling through overlap of molecular orbitals and to provide continuous transport pathways. While the angstrom-scale packing details can be studied using X-ray scattering methods, an understanding of the mesoscale, or the length scale over which smaller ordered regions connect, is much harder to achieve. Grain boundaries play an important role in semiconducting polymer thin films where the average grain size is much smaller than the total distance which charges must traverse in order to reach the electrodes in a device. The majority of semiconducting polymers adopt a lamellar packing structure in which the conjugated backbones align in parallel pi-stacks separated by the alkyl side-chains. Only two directions of transport are possible--along the conjugated backbone and in the pi-stacking direction. Currently, the discussion of transport between crystallites is centered around the idea of tie-chains, or "bridging" polymer chains connecting two ordered regions. However, as molecular structures become increasingly complex with the development of new donor-acceptor copolymers, additional forms of connectivity between ordered domains should be considered. High resolution transmission electron microscopy (HRTEM) is a powerful tool for directly imaging the crystalline grain boundaries in polymer and small-molecule thin films. Recently, structures

Self-organization, layered structure, and aggregation enhance persistence of a synthetic biofilm consortium.

Directory of Open Access Journals (Sweden)

Katie Brenner

Full Text Available Microbial consortia constitute a majority of the earth's biomass, but little is known about how these cooperating communities persist despite competition among community members. Theory suggests that non-random spatial structures contribute to the persistence of mixed communities; when particular structures form, they may provide associated community members with a growth advantage over unassociated members. If true, this has implications for the rise and persistence of multi-cellular organisms. However, this theory is difficult to study because we rarely observe initial instances of non-random physical structure in natural populations. Using two engineered strains of Escherichia coli that constitute a synthetic symbiotic microbial consortium, we fortuitously observed such spatial self-organization. This consortium forms a biofilm and, after several days, adopts a defined layered structure that is associated with two unexpected, measurable growth advantages. First, the consortium cannot successfully colonize a new, downstream environment until it self-organizes in the initial environment; in other words, the structure enhances the ability of the consortium to survive environmental disruptions. Second, when the layered structure forms in downstream environments the consortium accumulates significantly more biomass than it did in the initial environment; in other words, the structure enhances the global productivity of the consortium. We also observed that the layered structure only assembles in downstream environments that are colonized by aggregates from a previous, structured community. These results demonstrate roles for self-organization and aggregation in persistence of multi-cellular communities, and also illustrate a role for the techniques of synthetic biology in elucidating fundamental biological principles.

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

Science.gov (United States)

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

2016-11-03

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

Organic superconductors: A current overview, synthesis, structure and theory

International Nuclear Information System (INIS)

Wang, H.H.; Beno, M.A.; Carlson, K.D.; Geiser, U.; Kini, A.M.; Williams, J.M.

1990-01-01

To date, four types of crystal packing motifs (β, θ, κ and α) are known to lead to superconductivity in the BEDT-TTF based materials, where BEDT-TTF is bis(ethylenedithio)tetrathiafulvalene. The syntheses, crystal structures, physical properties and band electronic structures of these materials will be reviewed. Recent progress made in the oxygen containing analogue, BEDO-TTF [bis(ethylenedioxo)tetrathiofulvalene] will be presented. The implication and future prospect of organic superconductors will be discussed

Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

Energy Technology Data Exchange (ETDEWEB)

Chandonia, John-Marc; Kim, Sung-Hou

2006-03-15

Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

Energy Technology Data Exchange (ETDEWEB)

Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi [Department of Chemistry, Aalto University, FI-00076 Aalto (Finland)

2014-01-15

A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superlattice formation with all the organic precursors is verified through x-ray reflectivity studies. The effects of the interspersed organic layers/superlattice structure on the electrical and thermoelectric properties of ZnO are investigated through resistivity and Seebeck coefficient measurements at room temperature. The results suggest an increase in carrier concentration for small concentrations of organic layers, while higher concentrations seem to lead to rather large reductions in carrier concentration.

Organic/metal interfaces. Electronic and structural properties

Energy Technology Data Exchange (ETDEWEB)

Duhm, Steffen

2008-07-17

This work addresses several important topics of the field of organic electronics. The focus lies on organic/metal interfaces, which exist in all organic electronic devices. Physical properties of such interfaces are crucial for device performance. Four main topics have been covered: (i) the impact of molecular orientation on the energy levels, (ii) energy level tuning with strong electron acceptors, (iii) the role of thermodynamic equilibrium at organic/ organic homo-interfaces and (iv) the correlation of interfacial electronic structure and bonding distance. To address these issues a broad experimental approach was necessary: mainly ultraviolet photoelectron spectroscopy was used, supported by X-ray photoelectron spectroscopy, metastable atom electron spectroscopy, X-ray diffraction and X-ray standing waves, to examine vacuum sublimed thin films of conjugated organic molecules (COMs) in ultrahigh vacuum. (i) A novel approach is presented to explain the phenomenon that the ionization energy in molecular assemblies is orientation dependent. It is demonstrated that this is due to a macroscopic impact of intramolecular dipoles on the ionization energy in molecular assemblies. Furthermore, the correlation of molecular orientation and conformation has been studied in detail for COMs on various substrates. (ii) A new approach was developed to tune hole injection barriers ({delta}{sub h}) at organic/metal interfaces by adsorbing a (sub-) monolayer of an organic electron acceptor on the metal electrode. Charge transfer from the metal to the acceptor leads to a chemisorbed layer, which reduces {delta}{sub h} to the COM overlayer. This concept was tested with three acceptors and a lowering of {delta}{sub h} of up to 1.2 eV could be observed. (iii) A transition from vacuum-level alignment to molecular level pinning at the homo-interface between a lying monolayer and standing multilayers of a COM was observed, which depended on the amount of a pre-deposited acceptor. The

Strategic Defense Initiative Organization adaptive structures program overview

Science.gov (United States)

Obal, Michael; Sater, Janet M.

In the currently envisioned architecture none of the Strategic Defense System (SDS) elements to be deployed will receive scheduled maintenance. Assessments of performance capability due to changes caused by the uncertain effects of environments will be difficult, at best. In addition, the system will have limited ability to adjust in order to maintain its required performance levels. The Materials and Structures Office of the Strategic Defense Initiative Organization (SDIO) has begun to address solutions to these potential difficulties via an adaptive structures technology program that combines health and environment monitoring with static and dynamic structural control. Conceivable system benefits include improved target tracking and hit-to-kill performance, on-orbit system health monitoring and reporting, and threat attack warning and assessment.

Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China.

Science.gov (United States)

Tang, Xiangming; Li, Linlin; Shao, Keqiang; Wang, Boweng; Cai, Xianlei; Zhang, Lei; Chao, Jianying; Gao, Guang

2015-01-01

To elucidate the relationship between particle-attached (PA, ≥ 5.0 μm) and free-living (FL, 0.2-5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37,985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

Application of molecular spectroscopy to the determination of organic structures

International Nuclear Information System (INIS)

Leicknam, J.P.

1976-01-01

Some brief accounts are presented followed by a discussion about various physico-chemical techniques: Raman spectrometry, infrared spectrometry, resonance Raman spectrometry, conformational analysis and polarized Rayleigh diffusion. Applications of the Nuclear Magnetic Resonance to nucleotide structure in aqueous solution are described as well as some applications of neutron scattering to the study of organic structures [fr

The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics.

Science.gov (United States)

Lhomme, Emilie; Orain, Servane; Courcoux, Philippe; Onno, Bernard; Dousset, Xavier

2015-11-20

Fourteen bakeries located in different regions of France were selected. These bakers use natural sourdough and organic ingredients. Consequently, different organic sourdoughs used for the manufacture of French bread were studied by the enumeration of lactic acid bacteria (LAB) and 16S rRNA sequencing of the isolates. In addition, after DNA extraction the bacterial diversity was assessed by pyrosequencing of the 16S rDNA V1-V3 region. Although LAB counts showed significant variations (7.6-9.5log10CFU/g) depending on the sourdough studied, their identification through a polyphasic approach revealed a large predominance of Lactobacillus sanfranciscensis in all samples. In ten sourdoughs, both culture and independent methods identified L. sanfranciscensis as the dominant LAB species identified. In the remaining sourdoughs, culture methods identified 30-80% of the LAB as L. sanfranciscensis whereas more than 95% of the reads obtained by pyrosequencing belonged to L. sanfranciscensis. Other sub-dominant species, such as Lactobacillus curvatus, Lactobacillus hammesii, Lactobacillus paralimentarius, Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus sakei, were also identified. Quantification of L. sanfranciscensis by real-time PCR confirmed the predominance of this species ranging from 8.24 to 10.38log10CFU/g. Regarding the acidification characteristics, sourdough and related bread physico-chemical characteristics varied, questioning the involvement of sub-dominant species or L. sanfranciscensis intra-species diversity and/or the role of the baker's practices. Copyright © 2015 Elsevier B.V. All rights reserved.

Spatial and dynamic organization of molecular structures in the cell nucleus

NARCIS (Netherlands)

Brouwer, Anne-Kee

2010-01-01

In this thesis we attempt to provide a better understanding of the principles that underlie the spatial dynamic organization of the cell nucleus. Chapter 1 reviews the current status of knowledge about the structural and functional organization of the cell nucleus. In chapter 2, the development of a

Liposomes: structure, properties and methods of curative administration in organism

Directory of Open Access Journals (Sweden)

M. A. Kisyakova

2010-07-01

Full Text Available A review of data from scientific sources, devoted to problems of liposomes’ structure, properties and processes of formation was made. Advantages of liposomes used for medical purposes are shown. Methods of liposomes administration in an organism are characterised. Data on mechanisms of interaction between liposomes and cells, peculiarities of liposomes’ lipids composition and dependence of its tropism to definite organs and tissues are generalised.

Organic superalkalis with closed-shell structure and aromaticity

Science.gov (United States)

Srivastava, Ambrish Kumar

2018-06-01

Benzene (C6H6) and polycyclic hydrocarbons such as naphthalene (C10H8), anthracene (C14H10) and coronene (C24H12) are well known aromatic organic compounds. We study the substitution of Li replacing all H-atoms in these hydrocarbons using density functional method. The vertical ionisation energy of such lithiated species, i.e. C6Li6, C10Li8, C14Li10 and C24Li12 ranges 4.24-4.50 eV, which is lower than the ionisation energy (IE) of Li atom. Thus, these species may behave as superalkalis due to their lower IE than alkali metal. However, these lithiated species possess planar and closed-shell structure, unlike typical superalkalis. Furthermore, all Li-substituted species are aromatic although their degree of aromaticity is reduced as compared to corresponding hydrocarbon analogues. We have further explored the structure of C6Li6 as star-like, unlike its inorganic analogue B3N3Li6, which appears as fan-like structure. We have also demonstrated that the interaction of C6Li6 with a superhalogen (such as BF4) is similar to that of a typical superalkali (such as OLi3). This may further suggest that the proposed lithiated species may form a new class of closed-shell organic superalkalis with aromaticity.

Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral – Organic Interfaces

DEFF Research Database (Denmark)

Hakim, S. S.; Olsson, M. H. M.; Sørensen, H. O.

2017-01-01

The structure and the strength of organic compound adsorption on mineral surfaces are of interest for a number of industrial and environmental applications, oil recovery, CO2 storage and contamination remediation. Biomineralised calcite plays an essential role in the function of many organisms...... that control crystal growth with organic macromolecules. Carbonate rocks, composed almost exclusively of calcite, host drinking water aquifers and oil reservoirs. In this study, we examined the ordering behaviour of several organic compounds and the thickness of the adsorbed layers formed on calcite {10...... monolayers. The results of this work indicate that adhered organic compounds from the surrounding environment can affect the surface behaviour, depending on properties of the organic compound....

Research on Structure Innovation of Agricultural Organization in China's Southwestern Mountainous Regions

OpenAIRE

Du, Qiang; Luo, Min; Wang, Ping

2012-01-01

Taking agricultural organization in China's southwestern mountainous regions as research object, on the basis of analysis of the status quo of agricultural organization development in China's southwestern mountainous regions, we use related theoretical knowledge on economics and organization science, we probe into the process of innovation and mechanism of action concerning the structure of agricultural organization in China's southwestern mountainous regions over the past 30 years. Finally w...

Interracial Friendship and Structural Diversity: Trends for Greek, Religious, and Ethnic Student Organizations

Science.gov (United States)

Park, Julie J.; Kim, Young K.

2013-01-01

This article examines how peer interactions in college organizations (Greek, ethnic, and religious) affect interracial friendships, including whether peer interaction in student organizations mediates the relationship between structural diversity and interracial friendship. Involvement in ethnic student organizations was non-significant;…

Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane.

Science.gov (United States)

Jeong, Sanghyun; Cho, Kyungjin; Jeong, Dawoon; Lee, Seockheon; Leiknes, TorOve; Vigneswaran, Saravanamuthu; Bae, Hyokwan

2017-11-01

Four dual media filters (DMFs) were operated in a biofiltration mode with different engineered environments (DMF I and II: coagulation with/without acidification and DMF III and IV: without/with chlorination). Designed biofilm enrichment reactors (BERs) containing the removable reverse osmosis (RO) coupons, were connected at the end of the DMFs in parallel to analyze the biofilm on the RO membrane by DMF effluents. Filtration performances were evaluated in terms of dissolved organic carbon (DOC) and assimilable organic carbon (AOC). Organic foulants on the RO membrane were also quantified and fractionized. The bacterial community structures in liquid (seawater and effluent) and biofilm (DMF and RO) samples were analyzed using 454-pyrosequencing. The DMF IV fed with the chlorinated seawater demonstrated the highest reductions of DOC including LMW-N as well as AOC among the other DMFs. The DMF IV was also effective in reducing organic foulants on the RO membrane surface. The bacterial community structure was grouped according to the sample phase (i.e., liquid and biofilm samples), sampling location (i.e., DMF and RO samples), and chlorination (chlorinated and non-chlorinated samples). In particular, the biofilm community in the DMF IV differed from the other DMF treatments, suggesting that chlorination exerted as stronger selective pressure than pH adjustment or coagulation on the biofilm community. In the DMF IV, several chemoorganotrophic chlorine-resistant biofilm-forming bacteria such as Hyphomonas, Erythrobacter, and Sphingomonas were predominant, and they may enhance organic carbon degradation efficiency. Diverse halophilic or halotolerant organic degraders were also found in other DMFs (i.e., DMF I, II, and III). Various kinds of dominant biofilm-forming bacteria were also investigated in RO membrane samples; the results provided possible candidates that cause biofouling when DMF process is applied as the pretreatment option for the RO process. Copyright �

Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane

KAUST Repository

Jeong, Sanghyun

2017-07-25

Four dual media filters (DMFs) were operated in a biofiltration mode with different engineered environments (DMF I and II: coagulation with/without acidification and DMF III and IV: without/with chlorination). Designed biofilm enrichment reactors (BERs) containing the removable reverse osmosis (RO) coupons, were connected at the end of the DMFs in parallel to analyze the biofilm on the RO membrane by DMF effluents. Filtration performances were evaluated in terms of dissolved organic carbon (DOC) and assimilable organic carbon (AOC). Organic foulants on the RO membrane were also quantified and fractionized. The bacterial community structures in liquid (seawater and effluent) and biofilm (DMF and RO) samples were analyzed using 454-pyrosequencing. The DMF IV fed with the chlorinated seawater demonstrated the highest reductions of DOC including LMW-N as well as AOC among the other DMFs. The DMF IV was also effective in reducing organic foulants on the RO membrane surface. The bacterial community structure was grouped according to the sample phase (i.e., liquid and biofilm samples), sampling location (i.e., DMF and RO samples), and chlorination (chlorinated and non-chlorinated samples). In particular, the biofilm community in the DMF IV differed from the other DMF treatments, suggesting that chlorination exerted as stronger selective pressure than pH adjustment or coagulation on the biofilm community. In the DMF IV, several chemoorganotrophic chlorine-resistant biofilm-forming bacteria such as Hyphomonas, Erythrobacter, and Sphingomonas were predominant, and they may enhance organic carbon degradation efficiency. Diverse halophilic or halotolerant organic degraders were also found in other DMFs (i.e., DMF I, II, and III). Various kinds of dominant biofilm-forming bacteria were also investigated in RO membrane samples; the results provided possible candidates that cause biofouling when DMF process is applied as the pretreatment option for the RO process.

Integral Design workshops: organization, structure and testing

OpenAIRE

Zeiler, W Wim; Savanovic, P Perica

2010-01-01

The purpose of this paper is to achieve an understanding of design activities in the context of building design. The starting point is an overview of design research and design methodology. From the insights gained by this analysis of design in this specific context, we present an 'organization structure and design' workshop approach for collaborative multi-discipline design management. The workshops set-up, used to implement and to test the approach, are presented as well as the experiences ...

47 CFR 90.1408 - Organization and structure of the 700 MHz public/private partnership.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 5 2010-10-01 2010-10-01 false Organization and structure of the 700 MHz public/private partnership. 90.1408 Section 90.1408 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... Partnership § 90.1408 Organization and structure of the 700 MHz public/private partnership. (a) The Upper 700...

47 CFR 27.1308 - Organization and structure of the 700 MHz public/private partnership.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Organization and structure of the 700 MHz public/private partnership. 27.1308 Section 27.1308 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... Partnership § 27.1308 Organization and structure of the 700 MHz public/private partnership. (a) The Upper 700...

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

NARCIS (Netherlands)

Leite, Márcio F.A.; Pan, Yao; Bloem, Jaap; Berge, ten Hein; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments,

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

NARCIS (Netherlands)

Leite, M.F.A.; Pan, Y.; Bloem, J.; ten Berge, H.; Kuramae, E.E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments,

Synthesis and optical properties of novel organic-inorganic hybrid nanolayer structure semiconductors

International Nuclear Information System (INIS)

Zhang Sanjun; Lanty, Gaetan; Lauret, Jean-Sebastien; Deleporte, Emmanuelle; Audebert, Pierre; Galmiche, Laurent

2009-01-01

We report on the synthesis of some novel organic-inorganic hybrid 2D perovskite semiconductors (R-(CH 2 ) n NH 3 ) 2 PbX 4 . These semiconductors are self-assembled intercalation nanolayers and have a multi-quantum-well energy level structure. We systematically vary the characteristic of organic groups (R-(CH 2 ) n NH 3 + ) to study the relationship between their structures and the optical properties of (R-(CH 2 ) n NH 3 ) 2 PbX 4 . From optical absorption and photoluminescence spectroscopy experiments performed on series of samples, we find some trends of choosing the organic groups to improve the optical performance of (R-(CH 2 ) n NH 3 ) 2 PbX 4 . A new organic group, which allows synthesis of nanolayer perovskite semiconductors with quite high photoluminescence efficiency and better long-term stability, has been found.

Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

Directory of Open Access Journals (Sweden)

Bonten Marc JM

2010-04-01

Full Text Available Abstract Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI, which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

Science.gov (United States)

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Developing organization structure of retail enterprises (on the example of the Czech Republic

Directory of Open Access Journals (Sweden)

Aleksandr L. Bobkov

2017-01-01

Full Text Available The goal of the research is to prove repetitiveness of changes in the organization structure of commercial enterprises. With regard to the goals of the research, such scientifically well-known paired notions as vertical and horizontal; high and flat; mechanical and organic can be considered as two basic types of organizational structures. The authors’ hypothesis is that these two types of structures – consequent and parallel – replace each other dialectically, and change qualitatively in the process of enterprises growth, but, at the same time, they maintain their constitutive properties at each level of organizations development.The retail sector was chosen as the object of analysis, since the generalized organizational structure in it is characterized by separate sales outlets, which makes it possible to conduct statistical processing of data. In this context, enterprises of similar size (in terms of number of employees and sales volume and having similar (consequent or parallel organizational structures can make groups that form the aggregate of commercial organizations. Cluster analysis is a generally accepted method of defining groups joining objects that are homogeneous with respect to certain criteria. Cluster analysis is the means of exploratory analysis, meant for natural clustering of the initial data set into groups. The IBM SPSS Statistics software was used for defining clusters.The analysis was conducted according to the data of the Czech Republic retail enterprises. The economy of this Central-European country was chosen, because, on the one hand, it is a part of the common market of the United Europe, and, on the other hand, it preserves its national currency. The research data were obtained from the database of Albertina Gold Edition of Bisnode Česká republika, a.s., including enterprises of all the sectors. 1695 retail organizations of all sizes were chosen from the total trade organizations for the research.As a result

Structures of SAS-6 suggest its organization in centrioles.

Science.gov (United States)

van Breugel, Mark; Hirono, Masafumi; Andreeva, Antonina; Yanagisawa, Haru-aki; Yamaguchi, Shoko; Nakazawa, Yuki; Morgner, Nina; Petrovich, Miriana; Ebong, Ima-Obong; Robinson, Carol V; Johnson, Christopher M; Veprintsev, Dmitry; Zuber, Benoît

2011-03-04

Centrioles are cylindrical, ninefold symmetrical structures with peripheral triplet microtubules strictly required to template cilia and flagella. The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis. We determined the x-ray structure of the amino-terminal domain of SAS-6 from zebrafish, and we show that recombinant SAS-6 self-associates in vitro into assemblies that resemble cartwheel centers. Point mutations are consistent with the notion that centriole formation in vivo depends on the interactions that define the self-assemblies observed here. Thus, these interactions are probably essential to the structural organization of cartwheel centers.

The quality management system in leading organization of the integrated structure

Directory of Open Access Journals (Sweden)

Kunitsyn A. M.

2018-02-01

Full Text Available the article has analyzed the problem of integrated structure management. The author has noted that the implementation of recommendations outlined in the article will allow building and improving the quality management system in leading organization of integrated structure on a regular basis that meets the requirements.

Human and organization factors: engineering operating safety into offshore structures

International Nuclear Information System (INIS)

Bea, Robert G.

1998-01-01

History indicates clearly that the safety of offshore structures is determined primarily by the humans and organizations responsible for these structures during their design, construction, operation, maintenance, and decommissioning. If the safety of offshore structures is to be preserved and improved, then attention of engineers should focus on to how to improve the reliability of the offshore structure 'system,' including the people that come into contact with the structure during its life-cycle. This article reviews and discusss concepts and engineering approaches that can be used in such efforts. Two specific human factor issues are addressed: (1) real-time management of safety during operations, and (2) development of a Safety Management Assessment System to help improve the safety of offshore structures

Advanced organic composite materials for aircraft structures: Future program

Science.gov (United States)

1987-01-01

Revolutionary advances in structural materials have been responsible for revolutionary changes in all fields of engineering. These advances have had and are still having a significant impact on aircraft design and performance. Composites are engineered materials. Their properties are tailored through the use of a mix or blend of different constituents to maximize selected properties of strength and/or stiffness at reduced weights. More than 20 years have passed since the potentials of filamentary composite materials were identified. During the 1970s much lower cost carbon filaments became a reality and gradually designers turned from boron to carbon composites. Despite progress in this field, filamentary composites still have significant unfulfilled potential for increasing aircraft productivity; the rendering of advanced organic composite materials into production aircraft structures was disappointingly slow. Why this is and research and technology development actions that will assist in accelerating the application of advanced organic composites to production aircraft is discussed.

Perceptual organization in computer vision - A review and a proposal for a classificatory structure

Science.gov (United States)

Sarkar, Sudeep; Boyer, Kim L.

1993-01-01

The evolution of perceptual organization in biological vision, and its necessity in advanced computer vision systems, arises from the characteristic that perception, the extraction of meaning from sensory input, is an intelligent process. This is particularly so for high order organisms and, analogically, for more sophisticated computational models. The role of perceptual organization in computer vision systems is explored. This is done from four vantage points. First, a brief history of perceptual organization research in both humans and computer vision is offered. Next, a classificatory structure in which to cast perceptual organization research to clarify both the nomenclature and the relationships among the many contributions is proposed. Thirdly, the perceptual organization work in computer vision in the context of this classificatory structure is reviewed. Finally, the array of computational techniques applied to perceptual organization problems in computer vision is surveyed.

Evaluating the impact of investments in information technology on structural inertia in health organizations.

Science.gov (United States)

Bewley, Lee W

2010-01-01

Structural inertia is the overall capacity of an organization to adapt within a market environment. This paper reviews the impact of healthcare investments in information management/information technology (IM/IT) on the strategic management concept of structural inertia. Research indicates that healthcare executives should consider the relative state of structural inertia for their firms and match them with potential IM/IT solutions. Additionally, organizations should favorably consider IM/IT solutions that are comparatively less complex.

Stranski–Krastanov transition and self-organized structures in low-strained AlInN/GaN multilayer structures

International Nuclear Information System (INIS)

Krost, A; Berger, C; Moser, P; Bläsing, J; Dadgar, A; Hums, C; Hempel, T; Bastek, B; Veit, P; Christen, J

2011-01-01

Low-strained AlInN/GaN multilayers aimed as Bragg mirrors were grown by metal organic vapour phase epitaxy on GaN/Si(1 1 1). In such structures the upper AlInN/GaN interfaces show a considerable roughening on a nanometre scale whereas the lower ones appear flat as evaluated by cross-sectional electron and transmission electron microscopy. The roughening is attributed to a Stranski–Krastanov transition from two-dimensional layer-by-layer to three-dimensional island growth. In addition, a self-organized wavy-like surface morphology on a micrometre scale is observed in such structures which we discuss in terms of Grinfeld instability

Molecular orientation and electronic structure at organic heterojunction interfaces

Energy Technology Data Exchange (ETDEWEB)

Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

2015-10-01

Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

Expert systems for structure elucidation of organic molecules by spectral methods

International Nuclear Information System (INIS)

Elyashberg, Mikhail E

1999-01-01

The state-of-the-art of the investigations aimed at creating expert systems for establishing the structure of organic molecules from IR, 1 H and 13 C NMR spectra is analysed. Computer methods used for identification of molecular fragments, generation of their structure and spectra prediction are considered. Principles of the creation of modern expert systems and general strategy of solving structural problems are discussed. The bibliography includes 174 references.

Structural and optical studies of local disorder sensitivity in natural organic-inorganic self-assembled semiconductors

Energy Technology Data Exchange (ETDEWEB)

Vijaya Prakash, G; Pradeesh, K [Nanophotonics Lab, Department of Physics, Indian Institute of Technology Delhi, New Delhi (India); Ratnani, R; Saraswat, K [Department of Pure and Applied Chemistry, MDS University, Ajmer (India); Light, M E [School of Chemistry, University of Southampton, Southampton (United Kingdom); Baumberg, J J, E-mail: prakash@physics.iitd.ac.i [Nanophotonic Centre, Cavendish Laboratory, University Cambridge, Cambridge CB3 OHE (United Kingdom)

2009-09-21

The structural and optical spectra of two related lead iodide (PbI) based self-assembled hybrid organic-inorganic semiconductors are compared. During the synthesis, depending on the bridging of organic moiety intercalated between the PbI two-dimensional planes, different crystal structures are produced. These entirely different networks show different structural and optical features, including excitonic bandgaps. In particular, the modified organic environment of the excitons is sensitive to the local disorder both in single crystal and thin film forms. Such information is vital for incorporating these semiconductors into photonic device architectures.

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

Science.gov (United States)

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

2010-09-21

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

Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

Directory of Open Access Journals (Sweden)

Wolcott Randall D

2010-09-01

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

Influence of the crystallographic structure of the electrode surface on the structure of the electrical double layer and adsorption of organic molecules

International Nuclear Information System (INIS)

Kochorovski, Z.; Zagorska, I.; Pruzhkovska-Drakhal, R.; Trasatti, S.

1995-01-01

The results of systematic investigation of influence of crystal structure of Bi-, Sb- and Cd-electrode surfaces on regularities of double electric layer structure in aqueous and nonaqueous solutions of surface-nonactive electrolyte are given. Influence of electrode surface characteristics on adsorptive behaviour of different organic molecules has been studied. General regularities of of chemical nature influence and surface crystallographic structure on the double layer structure and on organic compounds adsorption have been established. 57 refs., 7 figs., 4 tabs

A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

Directory of Open Access Journals (Sweden)

Solis Julio

2010-10-01

Full Text Available Abstract Background Sweetpotato (Ipomoea batatas (L. Lam., a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST sequences and ~ 1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species. Results Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone Tanzania and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (I. batatas and 2 diploid (I. trifida accessions. Conclusions The sweetpotato gene index is a useful source for functionally annotated sweetpotato gene sequences that contains three times more gene sequence information for sweetpotato than previous EST assemblies. A searchable version of the gene index, including a blastn function, is available at http://www.cipotato.org/sweetpotato_gene_index.

Liquid crystal-based Mueller matrix spectral imaging polarimetry for parameterizing mineral structural organization.

Science.gov (United States)

Gladish, James C; Duncan, Donald D

2017-01-20

Herein, we discuss the remote assessment of the subwavelength organizational structure of a medium. Specifically, we use spectral imaging polarimetry, as the vector nature of polarized light enables it to interact with optical anisotropies within a medium, while the spectral aspect of polarization is sensitive to small-scale structure. The ability to image these effects allows for inference of spatial structural organization parameters. This work describes a methodology for revealing structural organization by exploiting the Stokes/Mueller formalism and by utilizing measurements from a spectral imaging polarimeter constructed from liquid crystal variable retarders and a liquid crystal tunable filter. We provide results to validate the system and then show results from measurements on a mineral sample.

A Task-Based Approach to Organization: Knowledge, Communication and Structure

OpenAIRE

Luis Garicano; Yanhui Wu

2010-01-01

We bridge a gap between organizational economics and strategy research by developing a task-based approach to analyze organizational knowledge, process and structure, and deriving testable implications for the relation between production and organizational structure. We argue that organization emerges to integrate disperse knowledge and to coordinate talent in production and is designed to complement the limitations of human ability. The complexity of the tasks undertaken determines the optim...

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

Science.gov (United States)

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

2017-10-25

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

Structure-directing effects of ionic liquids in the ionothermal synthesis of metal-organic frameworks.

Science.gov (United States)

Vaid, Thomas P; Kelley, Steven P; Rogers, Robin D

2017-07-01

Traditional synthesis of metal-organic frameworks (MOFs) involves the reaction of a metal-containing precursor with an organic linker in an organic solvent at an elevated temperature, in what is termed a 'solvothermal' reaction. More recently, many examples have been reported of MOF synthesis in ionic liquids (ILs), rather than an organic solvent, in 'ionothermal' reactions. The high concentration of both cations and anions in an ionic liquid allows for the formation of new MOF structures in which the IL cation or anion or both are incorporated into the MOF. Most commonly, the IL cation is included in the open cavities of the MOF, countering the anionic charge of the MOF framework itself and acting as a template around which the MOF structure forms. Ionic liquids can also serve other structure-directing roles, for example, when an IL containing a single enantiomer of a chiral anion leads to a homochiral MOF, even though the IL anion is not itself incorporated into the MOF. A comprehensive review of ionothermal syntheses of MOFs, and the structure-directing effects of the ILs, is given.

On structure of some laminated crystals with organic molecules

International Nuclear Information System (INIS)

Volodina, G.F.; Ivanova, V.Ya.; Malinovskij, T.I.

1982-01-01

A survey is made of papers dealing with intercalation of organic molecules into crystals of dihalcogenides of some transition metals (TaS 2 , TiS 2 , NbS 2 , ZrS 2 , TaSe 2 ), variation of their structure and physical properties. Among the used intercalates ammonia, pyridine, aniline and other aromatic amines proved to be most satisfactory from the viewpoint of reaction rate and product stability. A possibility is discussed of intercalation into PbI 2 and CdI 2 crystals that are of the same structural type as dihalcogenides

Systematic investigation of the effects of organic film structure on light emitting diode performance

Science.gov (United States)

Joswick, M. D.; Campbell, I. H.; Barashkov, N. N.; Ferraris, J. P.

1996-09-01

We present a systematic investigation of the effects of organic film structure on light emitting diode (LED) performance. Metal/organic film/metal LEDs were fabricated using a five ring, poly(phenylene vinylene) related oligomer as the active layer. The structure of the vacuum evaporated oligomer films was varied from amorphous to polycrystalline by changing the substrate temperature during deposition. The intrinsic properties of the oligomer films and the LED performance were measured. The measured intrinsic film properties include: optical absorption, photoluminescence (PL) spectra, PL lifetime, PL efficiency, and effective carrier mobility. The measured device characteristics include current-voltage, capacitance-voltage, electroluminescence (EL) efficiency, and the contact metal/organic film Schottky barrier heights. The optical absorption and PL properties of the films are weakly dependent on film structure but the effective carrier mobility decreases with increasing crystallinity. The EL quantum efficiency decreases by more than one order of magnitude, the drive voltage at a fixed current increases, and the electron Schottky barrier height increases as the crystallinity of the film is increased. The diode current-voltage characteristic is determined by the dominant hole current and the electroluminescence efficiency is controlled by the contact limited electron injection. These results demonstrate significant effects of organic film structure on the performance of organic LEDs.

Synthesis and optical properties of novel organic-inorganic hybrid nanolayer structure semiconductors

Energy Technology Data Exchange (ETDEWEB)

Zhang Sanjun; Lanty, Gaetan; Lauret, Jean-Sebastien [Laboratoire de Photonique Quantique et Moleculaire de l' Ecole Normale Superieure de Cachan, 61 avenue du President Wilson, 94235 Cachan (France); Deleporte, Emmanuelle, E-mail: Emmanuelle.Deleporte@lpqm.ens-cachan.fr [Laboratoire de Photonique Quantique et Moleculaire de l' Ecole Normale Superieure de Cachan, 61 avenue du President Wilson, 94235 Cachan (France); Audebert, Pierre; Galmiche, Laurent [Laboratoire de Photophysique et Photochimie Supramoleculaires et Macromoleculaires de l' Ecole Normale Superieure de Cachan, 61 avenue du President Wilson, 94235 Cachan (France)

2009-06-15

We report on the synthesis of some novel organic-inorganic hybrid 2D perovskite semiconductors (R-(CH{sub 2}){sub n}NH{sub 3}){sub 2}PbX{sub 4}. These semiconductors are self-assembled intercalation nanolayers and have a multi-quantum-well energy level structure. We systematically vary the characteristic of organic groups (R-(CH{sub 2}){sub n}NH{sub 3}{sup +}) to study the relationship between their structures and the optical properties of (R-(CH{sub 2}){sub n}NH{sub 3}){sub 2}PbX{sub 4}. From optical absorption and photoluminescence spectroscopy experiments performed on series of samples, we find some trends of choosing the organic groups to improve the optical performance of (R-(CH{sub 2}){sub n}NH{sub 3}){sub 2}PbX{sub 4}. A new organic group, which allows synthesis of nanolayer perovskite semiconductors with quite high photoluminescence efficiency and better long-term stability, has been found.

The function of advanced treatment process in a drinking water treatment plant with organic matter-polluted source water.

Science.gov (United States)

Lin, Huirong; Zhang, Shuting; Zhang, Shenghua; Lin, Wenfang; Yu, Xin

2017-04-01

To understand the relationship between chemical and microbial treatment at each treatment step, as well as the relationship between microbial community structure in biofilms in biofilters and their ecological functions, a drinking water plant with severe organic matter-polluted source water was investigated. The bacterial community dynamics of two drinking water supply systems (traditional and advanced treatment processes) in this plant were studied from the source to the product water. Analysis by 454 pyrosequencing was conducted to characterize the bacterial diversity in each step of the treatment processes. The bacterial communities in these two treatment processes were highly diverse. Proteobacteria, which mainly consisted of beta-proteobacteria, was the dominant phylum. The two treatment processes used in the plant could effectively remove organic pollutants and microbial polution, especially the advanced treatment process. Significant differences in the detection of the major groups were observed in the product water samples in the treatment processes. The treatment processes, particularly the biological pretreatment and O 3 -biological activated carbon in the advanced treatment process, highly influenced the microbial community composition and the water quality. Some opportunistic pathogens were found in the water. Nitrogen-relative microorganisms found in the biofilm of filters may perform an important function on the microbial community composition and water quality improvement.

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

Science.gov (United States)

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

2012-01-01

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

The molecular structure of the insoluble organic matter isolated from Murchison carbonaceous chondrite.

Science.gov (United States)

Robert, F.; Derenne, S.

2009-04-01

During these last 10 years, our group has characterized the various molecular moieties of the insoluble organic matter (IOM) isolated from carbonaceous meteorites with the aim of reconstructing its overall molecular structure. Indeed, a precise knowledge of the structure of an organic macromolecule contains irreplaceable information that traces its mechanisms of synthesis and its conditions of formation. Such a modelled structure will be presented. Carbonaceous chondrites contain up to 3 wt % of carbon that is under the form of soluble and insoluble fractions. The IOM, which constitutes more than 75 wt% of the bulk organic matter, was isolated from the bulk rock through successive acid dissolutions. The chemical structure of the isolated IOM has been studied by both (1) destructive and (2) non destructive methods. Methods include thermal and chemical degradations followed by GC/MS, spectroscopic techniques (nuclear magnetic resonance, Fourier transform infra red spectroscopy; X-ray absorption near-edge spectroscopy, electron paramagnetic resonance) along with high resolution transmission electron microscopy. Although each technique alone cannot provide definite information on the chemical structure of such a complex material, the combination of the results can be used to reconstruct the molecular structure of the IOM. The proposed structure accounts for all these measured parameters. The details of this structure reveal information of the conditions of its formation in space and allow to discuss the mechanisms of organo-synthesis in the cosmochemical context of the formation of the solar system.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

Science.gov (United States)

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada [version 2; referees: 2 approved

Directory of Open Access Journals (Sweden)

Christian Wurzbacher

2016-02-01

Full Text Available Most streams receive substantial inputs of allochthonous organic material in the form of leaves and twigs (CPOM, coarse particulate organic matter. Mechanical and biological processing converts this into fine particulate organic matter (FPOM. Other sources of particles include flocculated dissolved matter and soil particles. Fungi are known to play a role in the CPOM conversion process, but the taxonomic affiliations of these fungi remain poorly studied. The present study seeks to shed light on the composition of fungal communities on FPOM and CPOM as assessed in a natural stream in Nova Scotia, Canada. Maple leaves were exposed in a stream for four weeks and their fungal community evaluated through pyrosequencing. Over the same period, four FPOM size fractions were collected by filtration and assessed. Particles had much lower ergosterol contents than leaves, suggesting major differences in the extent of fungal colonization. Pyrosequencing documented a total of 821 fungal operational taxonomic units (OTU, of which 726 were exclusive to particles and 47 to leaf samples. Most fungal phyla were represented, including yeast lineages (e.g., Taphrinaceae and Saccharomycotina, Basidiomycota, Chytridiomycota and Cryptomycota, but several classes of Pezizomycontina (Ascomycota dominated. Cluster dendrograms clearly separated fungal communities from leaves and from particles. Characterizing fungal communities may shed some light on the processing pathways of fine particles in streams and broadens our view of the phylogenetic composition of fungi in freshwater ecosystems.

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

Science.gov (United States)

Subramaniam, Karthigeyan

2016-08-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and processes in social settings like classrooms thereby providing glimpses into the complex dynamics of teacher-students interactions, configurations, and conventions during collective meaning making and knowledge creation. Data included observations, interviews, and focus group interviews. Analysis revealed that the dominant participation structure evident within participants' instruction with computer technology was ( Teacher) initiation-( Student and Teacher) response sequences-( Teacher) evaluate participation structure. Three key events characterized the how participants organized this participation structure in their classrooms: setting the stage for interactive instruction, the joint activity, and maintaining accountability. Implications include the following: (1) teacher educators need to tap into the knowledge base that underscores science teachers' learning to teach philosophies when computer technology is used in instruction. (2) Teacher educators need to emphasize the essential idea that learning and cognition is not situated within the computer technology but within the pedagogical practices, specifically the participation structures. (3) The pedagogical practices developed with the integration or with the use of computer technology underscored by the teachers' own knowledge of classroom contexts and curriculum needs to be the focus for how students learn science content with computer technology instead of just focusing on how computer technology solely supports students learning of science content.

Metal–organic coordinated multilayer film formation: Quantitative analysis of composition and structure

Energy Technology Data Exchange (ETDEWEB)

Benson, Alexandra S.; Elinski, Meagan B.; Ohnsorg, Monica L.; Beaudoin, Christopher K.; Alexander, Kyle A.; Peaslee, Graham F.; DeYoung, Paul A.; Anderson, Mary E., E-mail: meanderson@hope.edu

2015-09-01

Metal–organic coordinated multilayers are self-assembled thin films fabricated by alternating solution–phase deposition of bifunctional organic molecules and metal ions. The multilayer film composed of α,ω-mercaptoalkanoic acid and Cu (II) has been the focus of fundamental and applied research with its robust reproducibility and seemingly simple hierarchical architecture. However, internal structure and composition have not been unambiguously established. The composition of films up to thirty layers thick was investigated using Rutherford backscattering spectrometry and particle induced X-ray emission. Findings show these films are copper enriched, elucidating a 2:1 ratio for the ion to molecule complexation at the metal–organic interface. Results also reveal that these films have an average layer density similar to literature values established for a self-assembled monolayer, indicating a robust and stable structure. The surface structures of multilayer films have been characterized by contact angle goniometry, ellipsometry, and scanning probe microscopy. A morphological transition is observed as film thickness increases from the first few foundational layers to films containing five or more layers. Surface roughness analysis quantifies this evolution as the film initially increases in roughness before obtaining a lower roughness comparable to the underlying gold substrate. Quantitative analysis of topographical structure and internal composition for metal–organic coordinated multilayers as a function of number of deposited layers has implications for their incorporation in the fields of photonics and nanolithography. - Highlights: • Layer-by-layer deposition is examined by scanning probe microscopy and ion beam analysis. • Film growth undergoes morphological evolution during foundational layer deposition. • Image analysis quantified surface features such as roughness, grain size, and coverage. • Molecular density of each film layer is found to

Hierarchical organization versus self-organization

OpenAIRE

Busseniers, Evo

2014-01-01

In this paper we try to define the difference between hierarchical organization and self-organization. Organization is defined as a structure with a function. So we can define the difference between hierarchical organization and self-organization both on the structure as on the function. In the next two chapters these two definitions are given. For the structure we will use some existing definitions in graph theory, for the function we will use existing theory on (self-)organization. In the t...

Confirmation of the Dimensional Adjustment Model of Organizational Structure in Municipal Sports Organizations

OpenAIRE

Sofia Nikolaidou; Vasilis Gialamas; Georgia Yfantidou; George Costa; George Mavrommatis

2015-01-01

The presence of municipal sport organizations indicates the priority, which is given from the local authority in the well-being of citizens. On the other hand, it constitutes the basis upon which sports are built in national level. The whole body of the organizations has an organizational structure. The organizational structure is a system of registration of employment and the relations that govern them. The basic dimensions are: concentration, complexity and formalization. The purpose of thi...

One-dimensional nonlinear self-organized structures in dusty plasmas

International Nuclear Information System (INIS)

Tsytovich, V.N.

2000-01-01

Dusty plasmas, which are open systems, can form stable one-dimensional self-organized structures. Absorption of plasma by dust particles results in the plasma flux from the plasma regions where the dust is absent. It is found that, in a one-dimensional dust layer, this flux is completely determined by the number of dust particles per unit area of the layer surface. This number determines all of the other parameters of the steady-state dust structure; in particular, it determines the spatial distributions of the dust density, dust charge, electron and ion densities, and ion drift velocity. In these structures, a force and electrostatic balance is established that ensures the necessary conditions for confining the dust and plasma particles in the structure. The equilibrium structures exist only for subthermal ion flow velocities. This criterion determines the maximum possible number of dust particles per unit area in the steady-state structure. The structures have a universal thickness, and the dust density changes sharply at the edge of the structure. The structures with a size either less than or larger than the ion mean free path with respect to ion-neutral collisions, quasi-neutral and charged structures, and soliton- and anti-soliton-like structures are investigated. Laboratory experiments and observations in extraterrestrial plasma formation are discussed in relation to dust structures

Structural and functional rich club organization of the brain in children and adults.

Directory of Open Access Journals (Sweden)

David S Grayson

Full Text Available Recent studies using Magnetic Resonance Imaging (MRI have proposed that the brain's white matter is organized as a rich club, whereby the most highly connected regions of the brain are also highly connected to each other. Here we use both functional and diffusion-weighted MRI in the human brain to investigate whether the rich club phenomena is present with functional connectivity, and how this organization relates to the structural phenomena. We also examine whether rich club regions serve to integrate information between distinct brain systems, and conclude with a brief investigation of the developmental trajectory of rich-club phenomena. In agreement with prior work, both adults and children showed robust structural rich club organization, comprising regions of the superior medial frontal/dACC, medial parietal/PCC, insula, and inferior temporal cortex. We also show that these regions were highly integrated across the brain's major networks. Functional brain networks were found to have rich club phenomena in a similar spatial layout, but a high level of segregation between systems. While no significant differences between adults and children were found structurally, adults showed significantly greater functional rich club organization. This difference appeared to be driven by a specific set of connections between superior parietal, insula, and supramarginal cortex. In sum, this work highlights the existence of both a structural and functional rich club in adult and child populations with some functional changes over development. It also offers a potential target in examining atypical network organization in common developmental brain disorders, such as ADHD and Autism.

Evolution of self-organization in nano-structured PVD coatings under extreme tribological conditions

Energy Technology Data Exchange (ETDEWEB)

Fox-Rabinovich, G., E-mail: gfox@mcmaster.ca [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Kovalev, A. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Aguirre, M.H. [Laboratory of Advanced Microscopy, Institute of Nanoscience of Aragón, University of Zaragoza, 50018 Zaragoza (Spain); Yamamoto, K. [Materials Research Laboratory, Kobe Steel Ltd, 1-5-5 Takatsuda-dai, Nishi-ku, Kobe 651-2271, Hyogo (Japan); Veldhuis, S. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Gershman, I. [All-Russian Railway Research Institute, 10 Third Mytishchinskaya Street, Moscow 29851 (Russian Federation); Rashkovskiy, A. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Endrino, J.L. [Albengoa Research, Energia Solar 1, Palmas Altas, Seville 41014 (Spain); Beake, B. [Micro Materials Limited, Willow House, Yale Business Village, Ellice Way, Wrexham LL13 7YL (United Kingdom); Dosbaeva, G. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Wainstein, D. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Yuan, Junifeng; Bunting, J.W. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada)

2014-04-01

Highlights: • The evolution of self-organization under extreme frictional conditions has been studied. • Comprehensive characterization of the tribo-films was made using various surface analytical techniques. • During the running-in stage, mullite tribo-ceramics predominate on the surface of the nano-multilayer coating, establishing a functional hierarchy within the layer of tribo-films. • It is possible to control tribo-film evolution during self-organization by means of an increase in structural complexity and the non-equilibrium state of the surface engineered layer. - Abstract: The evolution of the self-organization process where dissipative structures are formed under the extreme frictional conditions associated with high performance dry machining of hardened steels has been studied in detail. The emphasis was on the progressive studies of surface transformations within multilayer and monolayer TiAlCrSiYN-based PVD coatings during the running-in stage of wear when self-organization process occurs. The coating layer was characterized by high resolution electron energy-loss spectroscopy (HREELS). It is shown that the nano-multilayer coating possesses higher non-equilibrium structure in comparison to the monolayer. Comprehensive studies of the tribo-films (dissipative structures) formed on the friction surface were made using a number of advanced surface characterization techniques such as X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES). The data obtained for the tribo-films was combined with the detailed TEM studies of the structural and phase transformations within the underlying coating layer. This data was related to the micro-mechanical characteristics of the coating layer and its wear resistance. It was demonstrated that the evolution of the self-organization process is strongly controlled by the characteristics of the tribo-films formed at different stages of the wear process. Within running-in stage (after

Structure-directing effects of ionic liquids in the ionothermal synthesis of metal–organic frameworks

Directory of Open Access Journals (Sweden)

Thomas P. Vaid

2017-07-01

Full Text Available Traditional synthesis of metal–organic frameworks (MOFs involves the reaction of a metal-containing precursor with an organic linker in an organic solvent at an elevated temperature, in what is termed a `solvothermal' reaction. More recently, many examples have been reported of MOF synthesis in ionic liquids (ILs, rather than an organic solvent, in `ionothermal' reactions. The high concentration of both cations and anions in an ionic liquid allows for the formation of new MOF structures in which the IL cation or anion or both are incorporated into the MOF. Most commonly, the IL cation is included in the open cavities of the MOF, countering the anionic charge of the MOF framework itself and acting as a template around which the MOF structure forms. Ionic liquids can also serve other structure-directing roles, for example, when an IL containing a single enantiomer of a chiral anion leads to a homochiral MOF, even though the IL anion is not itself incorporated into the MOF. A comprehensive review of ionothermal syntheses of MOFs, and the structure-directing effects of the ILs, is given.

Systematic investigation of the effects of organic film structure on light emitting diode performance

Energy Technology Data Exchange (ETDEWEB)

Joswick, M.D.; Campbell, I.H. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Barashkov, N.N.; Ferraris, J.P. [The University of Texas at Dallas, Richardson, Texas 75080 (United States)

1996-09-01

We present a systematic investigation of the effects of organic film structure on light emitting diode (LED) performance. Metal/organic film/metal LEDs were fabricated using a five ring, poly(phenylene vinylene) related oligomer as the active layer. The structure of the vacuum evaporated oligomer films was varied from amorphous to polycrystalline by changing the substrate temperature during deposition. The intrinsic properties of the oligomer films and the LED performance were measured. The measured intrinsic film properties include: optical absorption, photoluminescence (PL) spectra, PL lifetime, PL efficiency, and effective carrier mobility. The measured device characteristics include current{endash}voltage, capacitance{endash}voltage, electroluminescence (EL) efficiency, and the contact metal/organic film Schottky barrier heights. The optical absorption and PL properties of the films are weakly dependent on film structure but the effective carrier mobility decreases with increasing crystallinity. The EL quantum efficiency decreases by more than one order of magnitude, the drive voltage at a fixed current increases, and the electron Schottky barrier height increases as the crystallinity of the film is increased. The diode current{endash}voltage characteristic is determined by the dominant hole current and the electroluminescence efficiency is controlled by the contact limited electron injection. These results demonstrate significant effects of organic film structure on the performance of organic LEDs. {copyright} {ital 1996 American Institute of Physics.}

Discussion on organization structure system of nuclear power projects in China

International Nuclear Information System (INIS)

Wang Zhi

2011-01-01

With the development of the nuclear power industry in China, several AE companies were born and now play a major role in building nuclear power projects in China and overseas. After studying current organization structure systems of all nuclear power AE companies in China and comparing with successful foreign ones, this paper proposes some approaches to optimize the structure. (author)

Internal structures of self-organized relaxed states and self-similar decay phase

International Nuclear Information System (INIS)

Kondoh, Yoshiomi

1992-03-01

A thought analysis on relaxation due to nonlinear processes is presented to lead to a set of general thoughts applicable to general nonlinear dynamical systems for finding out internal structures of the self-organized relaxed state without using 'invariant'. Three applications of the set of general thoughts to energy relaxations in resistive MHD plasmas, incompressible viscous fluids, and incompressible viscous MHD fluids are shown to lead to the internal structures of the self-organized relaxed states. It is shown that all of the relaxed states in these three dynamical systems are followed by self-similar decay phase without significant change of the spatial structure. The well known relaxed state of ∇ x B = ±λ B is shown to be derived generally in the low β plasma limit. (author)

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

Directory of Open Access Journals (Sweden)

Kimberly D Cephas

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

Self-organizing biochemical cycle in dynamic feedback with soil structure

Science.gov (United States)

Vasilyeva, Nadezda; Vladimirov, Artem; Smirnov, Alexander; Matveev, Sergey; Tyrtyshnikov, Evgeniy; Yudina, Anna; Milanovskiy, Evgeniy; Shein, Evgeniy

2016-04-01

In the present study we perform bifurcation analysis of a physically-based mathematical model of self-organized structures in soil (Vasilyeva et al., 2015). The state variables in this model included microbial biomass, two organic matter types, oxygen, carbon dioxide, water content and capillary pore size. According to our previous experimental studies, organic matter affinity to water is an important property affecting soil structure. Therefore, organic matter wettability was taken as principle distinction between organic matter types in this model. It considers general known biological feedbacks with soil physical properties formulated as a system of parabolic type non-linear partial differential equations with elements of discrete modeling for water and pore formation. The model shows complex behavior, involving emergence of temporal and spatial irregular auto-oscillations from initially homogeneous distributions. The energy of external impact on a system was defined by a constant oxygen level on the boundary. Non-linear as opposed to linear oxygen diffusion gives possibility of modeling anaerobic micro-zones formation (organic matter conservation mechanism). For the current study we also introduced population competition of three different types of microorganisms according to their mobility/feeding (diffusive, moving and fungal growth). The strongly non-linear system was solved and parameterized by time-optimized algorithm combining explicit and implicit (matrix form of Thomas algorithm) methods considering the time for execution of the evaluated time-step according to accuracy control. The integral flux of the CO2 state variable was used as a macroscopic parameter to describe system as a whole and validation was carried out on temperature series of moisture dependence for soil heterotrophic respiration data. Thus, soil heterotrophic respiration can be naturally modeled as an integral result of complex dynamics on microscale, arising from biological processes

The Changing Needs for Higher Education Organizations Structure in Vietnam: Evidence from Japanese, Taiwanese, and Thai Universities

Directory of Open Access Journals (Sweden)

Minh-Quang Duong

2013-02-01

Full Text Available Organizational change is the process of changing the structure of the organization and the attitudes of members in the organization. During the last decade, both Vietnamese social and educational organizations have slowly changed in their organizational structure as a barrier to the development in the era of globalization and internationalization in Vietnam. This paper is an attempt to discuss the factors which affect Vietnamese higher educational organization. Discussions on the viewpoint of higher educational organization structure of Japan, Taiwan, and Thailand. Furthermore, this paper will contribute to improve educational management, and serve as a useful reference for future higher education’s school mergers.

Experimental research on the structural characteristics of high organic soft soil in different deposition ages

Science.gov (United States)

Liu, Fei; Lin, Guo-he

2018-03-01

High organic soft soil, which is distributed at Ji Lin province in China, has been studied by a lot of scholars. In the paper, structural characteristics with different deposition ages have been researched by experimental tests. Firstly, the characteristics of deposition age, degree of decompositon, high-pressure consolidation and microstructure have been measured by a series of tests. Secondly, structural strengths which were deposited in different ages, have been carried out to test the significant differences of stress-strain relations between remoulded and undisturbed high organic soft soil samples. Results showed that high organic soft soil which is deposited at different ages will influence its structural characteristics.

Single-Walled Carbon-Nanotubes-Based Organic Memory Structures

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Sundes Fakher

2016-09-01

Full Text Available The electrical behaviour of organic memory structures, based on single-walled carbon-nanotubes (SWCNTs, metal–insulator–semiconductor (MIS and thin film transistor (TFT structures, using poly(methyl methacrylate (PMMA as the gate dielectric, are reported. The drain and source electrodes were fabricated by evaporating 50 nm gold, and the gate electrode was made from 50 nm-evaporated aluminium on a clean glass substrate. Thin films of SWCNTs, embedded within the insulating layer, were used as the floating gate. SWCNTs-based memory devices exhibited clear hysteresis in their electrical characteristics (capacitance–voltage (C–V for MIS structures, as well as output and transfer characteristics for transistors. Both structures were shown to produce reliable and large memory windows by virtue of high capacity and reduced charge leakage. The hysteresis in the output and transfer characteristics, the shifts in the threshold voltage of the transfer characteristics, and the flat-band voltage shift in the MIS structures were attributed to the charging and discharging of the SWCNTs floating gate. Under an appropriate gate bias (1 s pulses, the floating gate is charged and discharged, resulting in significant threshold voltage shifts. Pulses as low as 1 V resulted in clear write and erase states.

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

Science.gov (United States)

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

2014-12-01

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

Correlating electronic and geometric structures of organic films and interfaces by means of synchrotron radiation based techniques

International Nuclear Information System (INIS)

Yamane, Hiroyuki

2013-01-01

The electronic structure of organic thin films and interfaces plays a crucial role in the performance of optoelectronic devices using organic semiconductors, and is seriously dominated by the geometric film/interface structure due to the anisotropic spatial distribution of molecular orbitals. This paper briefly reviews the recent progress of the examination of correlating electronic structure and geometric structure of archetypal organic semiconductor thin films and interfaces by using spectroscopic experiments with synchrotron radiation such as angle-resolved photoelectron spectroscopy, x-ray absorption spectroscopy, and x-ray standing wave. (author)

Effects of organic versus conventional arable farming on soil structure and organic matter dynamics in a marine loam in the Netherlands

NARCIS (Netherlands)

Pulleman, M.M.; Jongmans, A.G.; Marinissen, J.C.Y.; Bouma, J.

2003-01-01

We compared the effects of conventional and organic arable farming on soil organic matter (SOM) content, soil structure, aggregate stability and C and N mineralization, which are considered important factors in defining sustainable land management. Within one soil series, three different farming

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

Science.gov (United States)

Landis, W. J.

1995-01-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Impact of organic and inorganic nanomaterials in the soil microbial community structure

Energy Technology Data Exchange (ETDEWEB)

Nogueira, Veronica; Lopes, Isabel [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rocha-Santos, Teresa [ISEIT/Viseu, Instituto Piaget, Estrada do Alto do Gaio, Galifonge, 3515-776 Lordosa, Viseu (Portugal); Santos, Ana L. [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rasteiro, Graca M.; Antunes, Filipe [CIEPQPF, Department of Chemical Engineering, Faculty of Science and Technology, Polo II, University of Coimbra, 3030-290 Coimbra (Portugal); Goncalves, Fernando; Soares, Amadeu M.V.M.; Cunha, Angela; Almeida, Adelaide [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Gomes, Newton N.C.M., E-mail: gomesncm@ua.pt [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Pereira, Ruth [Department of Biology, Faculty of Science, University of Porto, Rua do Campo Alegre 4169-007 Porto (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal)

2012-05-01

In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6-V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO{sub 2}), titanium silicon oxide (TiSiO{sub 4}), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO{sub 2}, CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: Black-Right-Pointing-Pointer Organic and inorganic nanomaterials on soil microbial community. Black-Right-Pointing-Pointer Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. Black-Right-Pointing-Pointer All the organic nanomaterials, TiO{sub 2} and gold nanorods significantly affected the structural diversity.

Structural and functional organization of ribosomal genes within the mammalian cell nucleolus.

Science.gov (United States)

Derenzini, Massimo; Pasquinelli, Gianandrea; O'Donohue, Marie-Françoise; Ploton, Dominique; Thiry, Marc

2006-02-01

Data on the in situ structural-functional organization of ribosomal genes in the mammalian cell nucleolus are reviewed here. Major findings on chromatin structure in situ come from investigations carried out using the Feulgen-like osmium ammine reaction as a highly specific electron-opaque DNA tracer. Intranucleolar chromatin shows three different levels of organization: compact clumps, fibers ranging from 11 to 30 nm, and loose agglomerates of extended DNA filaments. Both clumps and fibers of chromatin exhibit a nucleosomal organization that is lacking in the loose agglomerates of extended DNA filaments. In fact, these filaments constantly show a thickness of 2-3 nm, the same as a DNA double-helix molecule. The loose agglomerates of DNA filaments are located in the fibrillar centers, the interphase counterpart of metaphase NORs, therefore being constituted by ribosomal DNA. The extended, non-nucleosomal configuration of this rDNA has been shown to be independent of transcriptional activity and characterizes ribosome genes that are either transcribed or transcriptionally silent. Data reviewed are consistent with a model of control for ribosome gene activity that is not mediated by changes in chromatin structure. The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.

Impact of organic and inorganic nanomaterials in the soil microbial community structure

International Nuclear Information System (INIS)

Nogueira, Verónica; Lopes, Isabel; Rocha-Santos, Teresa; Santos, Ana L.; Rasteiro, Graça M.; Antunes, Filipe; Gonçalves, Fernando; Soares, Amadeu M.V.M.; Cunha, Angela; Almeida, Adelaide; Gomes, Newton N.C.M.; Pereira, Ruth

2012-01-01

In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6–V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO 2 ), titanium silicon oxide (TiSiO 4 ), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO 2 , CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: ► Organic and inorganic nanomaterials on soil microbial community. ► Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. ► All the organic nanomaterials, TiO 2 and gold nanorods significantly affected the structural diversity.

Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends.

Science.gov (United States)

Marzorati, Massimo; Maignien, Lois; Verhelst, An; Luta, Gabriela; Sinnott, Robert; Kerckhof, Frederiek Maarten; Boon, Nico; Van de Wiele, Tom; Possemiers, Sam

2013-02-01

The combination of a Simulator of the Human Intestinal Microbial Ecosystem with ad hoc molecular techniques (i.e. pyrosequencing, denaturing gradient gel electrophoresis and quantitative PCR) allowed an evaluation of the extent to which two plant polysaccharide supplements could modify a complex gut microbial community. The presence of Aloe vera gel powder and algae extract in product B as compared to the standard blend (product A) improved its fermentation along the entire simulated colon. The potential extended effect of product B in the simulated distal colon, as compared to product A, was confirmed by: (i) the separate clustering of the samples before and after the treatment in the phylogenetic-based dendrogram and OTU-based PCoA plot only for product B; (ii) a higher richness estimator (+33 vs. -36 % of product A); and (iii) a higher dynamic parameter (21 vs. 13 %). These data show that the combination of well designed in vitro simulators with barcoded pyrosequencing is a powerful tool for characterizing changes occurring in the gut microbiota following a treatment. However, for the quantification of low-abundance species-of interest because of their relationship to potential positive health effects (i.e. bifidobacteria or lactobacilli)-conventional molecular ecological approaches, such as PCR-DGGE and qPCR, still remain a very useful complementary tool.

Metal-ion interactions and the structural organization of Sepia eumelanin.

Science.gov (United States)

Liu, Yan; Simon, John D

2005-02-01

The structural organization of melanin granules isolated from ink sacs of Sepia officinalis was examined as a function of metal ion content by scanning electron microscopy and atomic force microscopy. Exposing Sepia melanin granules to ethelenediaminetetraacetic acid (EDTA) solution or to metal salt solutions changed the metal content in the melanin, but did not alter granular morphology. Thus ionic forces between the organic components and metal ions in melanin are not required to sustain the natural morphology once the granule is assembled. However, when aqueous suspensions of Sepia melanin granules of varying metal content are ultra-sonicated, EDTA-washed and Fe-saturated melanin samples lose material to the solution more readily than the corresponding Ca(II) and Mg(II)-loaded samples. The solubilized components are found to be 5,6-dihydroxyindole-2-carboxylic acid (DHICA)-rich constituents. Associated with different metal ions, Na(I), Ca(II) and Mg(II) or Fe(III), these DHICA-rich entities form distinct two-dimensional aggregation structures when dried on the flat surface of mica. The data suggest multiply-charged ions play an important role in assisting or templating the assembly of the metal-free organic components to form the three-dimensional substructure distributed along the protein scaffold within the granule.

Supramolecular Assembly of Calcium Metal - Organic Frameworks with Structural Transformation

Czech Academy of Sciences Publication Activity Database

Liang, P.-Ch.; Liu, H.-K.; Yeh, Ch.-T.; Lin, Ch.-H.; Zima, Vítězslav

2011-01-01

Roč. 11, č. 3 (2011), 699-708 ISSN 1528-7483 R&D Projects: GA ČR GA203/08/0208 Institutional research plan: CEZ:AV0Z40500505 Keywords : metal - organic frameworks * calcium * structure Subject RIV: CA - Inorganic Chemistry Impact factor: 4.720, year: 2011

Self-organized structures in a superorganism: do ants “behave” like molecules?

Science.gov (United States)

Detrain, Claire; Deneubourg, Jean-Louis

2006-09-01

While the striking structures (e.g. nest architecture, trail networks) of insect societies may seem familiar to many of us, the understanding of pattern formation still constitutes a challenging problem. Over the last two decades, self-organization has dramatically changed our view on how collective decision-making and structures may emerge out of a population of ant workers having each their own individuality as well as a limited access to information. A variety of collective behaviour spontaneously outcome from multiple interactions between nestmates, even when there is no directing influence imposed by an external template, a pacemaker or a leader. By focussing this review on foraging structures, we show that ant societies display some properties which are usually considered in physico-chemical systems, as typical signatures of self-organization. We detail the key role played by feed-back loops, fluctuations, number of interacting units and sensitivity to environmental factors in the emergence of a structured collective behaviour. Nonetheless, going beyond simple analogies with non-living self-organized patterns, we stress on the specificities of social structures made of complex living units of which the biological features have been selected throughout the evolution depending on their adaptive value. In particular, we consider the ability of each ant individual to process information about environmental and social parameters, to accordingly tune its interactions with nestmates and ultimately to determine the final pattern emerging at the collective level. We emphasize on the parsimony and simplicity of behavioural rules at the individual level which allow an efficient processing of information, energy and matter within the whole colony.

Self-Structured Organizing Single-Input CMAC Control for Robot Manipulator

Directory of Open Access Journals (Sweden)

ThanhQuyen Ngo

2011-09-01

Full Text Available This paper represents a self-structured organizing single-input control system based on differentiable cerebellar model articulation controller (CMAC for an n-link robot manipulator to achieve the high-precision position tracking. In the proposed scheme, the single-input CMAC controller is solely used to control the plant, so the input space dimension of CMAC can be simplified and no conventional controller is needed. The structure of single-input CMAC will also be self-organized; that is, the layers of single-input CMAC will grow or prune systematically and their receptive functions can be automatically adjusted. The online tuning laws of single-input CMAC parameters are derived in gradient-descent learning method and the discrete-type Lyapunov function is applied to determine the learning rates of proposed control system so that the stability of the system can be guaranteed. The simulation results of robot manipulator are provided to verify the effectiveness of the proposed control methodology.

Studies on structure and organization of calcium carbonate deposits in algae

Digital Repository Service at National Institute of Oceanography (India)

Kerkar, V.; Untawale, A.G.

The structure and organization of calcium carbonate deposits is studied in species of Halimeda, Udotea, Neomeris (Chlorophyta) and Padina (Phaeophyta). It was found that in Halimeda aragonite deposition takes place outside the cell wall...

Analysis of self-organized In(Ga)As quantum structures with the scanning transmission electron microscope

International Nuclear Information System (INIS)

Sauerwald, Andres

2008-01-01

Aim of this thesis was to apply the analytical methods of the scanning transmission electron microscopy to the study of self-organized In(Ga)As quantum structures. With the imaging methods Z contrast and bright field (position resolutions in the subnanometer range) and especially with the possibilities of the quantitative chemical EELS analysis of the scanning transmission electron microscope (STEM) fundamental questions concerning morphology and chemical properties of self-organized quantum structures should be answered. By the high position resolution of the STEM among others essentail morphological and structural parameters in the growth behaviour of ''dot in a well'' (DWell) structures and of vertically correlated quantum dots (QDs) could be analyzed. For the optimization of DWell structures samples were studied, the nominal InAs-QD growth position was directedly varied within the embedding InGaAs quantum wells. The STEM offers in connection with the EELS method a large potential for the chemical analysis of quantum structures. Studied was a sample series of self-organized InGaAs/GaAs structures on GaAs substrate, the stress of which was changed by varying the Ga content of the INGaAs material between 2.4 % and 4.3 % [de

Structural organization of the transfer RNA operon I of Vibrio cholerae

Indian Academy of Sciences (India)

Unknown

[Ghatak A, Majumdar A and Ghosh R K 2005 Structural organization of the transfer RNA operon I of Vibrio cholerae: Differences ..... clonal relationship are of utmost importance. ... rately derived from environmental, nontoxigenic, non-O1.

General scheme for elucidating the structure of organic compounds using spectroscopic and spectrometric methods

International Nuclear Information System (INIS)

Ribeiro, Carlos Magno R.; Souza, Nelson Angelo de

2007-01-01

This work describes a systematic method to be applied in undergraduate courses of organic chemistry, correlating infrared spectra, hydrogen and carbon-13 nuclear magnetic resonance, and mass spectra. To this end, a scheme and a table were developed to conduct the elucidation of the structure of organic compounds initially using infrared spectra. Interpretation of hydrogen and carbon-13 nuclear magnetic resonance spectra and of mass spectra is used to confirm the proposed structure. (author)

Structure transformations of endocrine system organs during adaptation to increased radioactivity

International Nuclear Information System (INIS)

Ermakova, O.V.

2004-01-01

It is well known that during ecological monitoring of contaminated territories registration of early abnormalities in an organism is hampered by man-caused influence of habitat. Under these circumstances study of both structural and functional changes in organs and tissues of rodents inhabiting radioactive contaminated territories is of great importance. Study of structural features of endocrine glands, hormones of which trigger the process of active adaptive changes in an organism, is very important in radioecological surveys. Basing on long-term study of voles we have determined that long-term living by rodents on the territories characterized by increased natural and artificial radioactivity (radium contaminated fields in the Komi Republic and 30-km zone of Chernobyl APS) substantially influences morpho-functional state of endocrine system organs, causing quantitative and qualitative changes. It is demonstrated that population processes modify biological consequences of small doze chronic ionizing radiation in habitat. We noticed the following: high heterogeneity of histological changes of thyroid gland and adrenal gland as a response to radioactive habitat contamination; disorder of interconnection among different links of endocrine system; dependence of radiation effects on gender, age, degree and character of radiation contamination of a habitat as well as duration of radioactive influence. We have got data on morphological characteristics of thyroid gland and adrenal gland during different phases of population amount of this kind of rodents. It was discovered that effectiveness of radiation influence is not the same during different periods of population cycle. Presence of voles on the territories characterized by increased radioactivity causes chronic tension of adrenal cortex (increasing of the organ mass, enlarging of thickness of zona fasciculata and zona reticularis). Destructive-necrotic processes combine with manifestation of reparative regeneration

Prerequisites for Amplicon Pyrosequencing of Microbial Methanol Utilizers in the Environment

Directory of Open Access Journals (Sweden)

Steffen eKolb

2013-09-01

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

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

Science.gov (United States)

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

2013-10-01

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

A METHOD FOR CREATING STRUCTURES OR DEVICES USING AN ORGANIC ICE RESIST

DEFF Research Database (Denmark)

2017-01-01

The invention relates to a method for creating an organic resist on a surface of a cooled substrate, the method comprising the steps of condensing a vapour into a solid film on the surface of the cooled substrate; patterning at least part of the solid film by exposing selected portions of said...... solid film to at least one electron beam thereby creating the organic resist on 5 the surface of the cooled substrate in accordance with a predetermined pattern; wherein the created organic resist remains essentially intact at ambient conditions; and using the created organic resist as a mask...... for creating semiconductor structures and/or semiconductor devices....

Synthesis, structural, thermal and optical studies of inorganic-organic hybrid semiconductors, R-PbI4

Science.gov (United States)

Pradeesh, K.; Nageswara Rao, K.; Vijaya Prakash, G.

2013-02-01

Wide varieties of naturally self-assembled two-dimensional inorganic-organic (IO) hybrid semiconductors, (4-ClC6H4NH3)2PbI4, (C6H9C2H4NH3)2PbI4, (CnH2n+1NH3)2PbI4 (where n = 12, 16, 18), (CnH2n-1NH3)2PbI4 (where n = 3, 4, 5), (C6H5C2H4NH3)2PbI4, NH3(CH2)12NH3PbI4, and (C4H3SC2H4NH3)2PbI4, were fabricated by intercalating structurally diverse organic guest moieties into lead iodide perovskite structure. The crystal packing of all these fabricated IO-hybrids comprises of well-ordered organic and inorganic layers, stacked-up alternately along c-axis. Almost all these hybrids are thermally stable upto 200 °C and show strong room-temperature exciton absorption and photoluminescence features. These strongly confined optical excitons are highly influenced by structural deformation of PbI matrix due to the conformation of organic moiety. A systematic correlation of optical exciton behavior of IO-hybrids with the organic/inorganic layer thicknesses, intercalating organic moieties, and various structural disorders were discussed. This systematic study clearly suggests that the PbI layer crumpling is directly responsible for the tunability of optical exciton energy.

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

Science.gov (United States)

Le, Huong T.; Ho, Cuong T.; Trinh, Quan H.; Trinh, Duc A.; Luu, Minh T. N.; Tran, Hai S.; Orange, Didier; Janeau, Jean L.; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

2016-01-01

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

Organic-Inorganic Hydrophobic Nanocomposite Film with a Core-Shell Structure

Directory of Open Access Journals (Sweden)

Peng Liu

2016-12-01

Full Text Available A method to prepare novel organic-inorganic hydrophobic nanocomposite films was proposed by a site-specific polymerization process. The inorganic part, the core of the nanocomposite, is a ternary SiO2–Al2O3–TiO2 nanoparticles, which is grafted with methacryloxy propyl trimethoxyl silane (KH570, and wrapped by fluoride and siloxane polymers. The synthesized samples are characterized by transmission electron microscopy (TEM, Fourier transform infrared (FTIR spectrscopy, X-ray diffractometry (XRD, contact angle meter (CA, and scanning electron microscope (SEM. The results indicate that the novel organic-inorganic hydrophobic nanocomposite with a core-shell structure was synthesized successfully. XRD analysis reveals the nanocomposite film has an amorphous structure, and FTIR analysis indicates the nanoparticles react with a silane coupling agent (methacryloxy propyl trimethoxyl silane KH570. Interestingly, the morphology of the nanoparticle film is influenced by the composition of the core. Further, comparing with the film synthesized by silica nanoparticles, the film formed from SiO2–Al2O3–TiO2 nanoparticles has higher hydrophobic performance, i.e., the contact angle is greater than 101.7°. In addition, the TEM analysis reveals that the crystal structure of the particles can be changed at high temperatures.

Social Capital in Organizations - Beyond Structure and Metaphor

DEFF Research Database (Denmark)

Waldstrøm, Christian

2003-01-01

a consistent, bridging theory. Finally, there is a lack of understanding on how social capital develops over time and the potential benefits of taking a life-cycle view of social capital. In conclusion, the field of social capital in organizations still needs a consistent and coordinated research effort......The importance and usefulness of social capital as a concept in the study of organizations have been established by a large body of research. The aim of this paper is to review the concept of social capital in an organizational context, and it identifies five main issues that need to be addressed...... in future research before social capital can move definitively beyond being merely a metaphor for advantage. First, the unresolved issue of causality is a barrier in the study of social structure and social capital alike, and hampers both measuring scales and implications drawn from empirical research...

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

Science.gov (United States)

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

2014-11-01

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

Experimental investigation of multiple self-organized structures in plasma

International Nuclear Information System (INIS)

Ivan, L. M.; Gaman, C.; Aflori, M.; Mihai-Plugaru, M.; Dimitriu, D.G.; Lozneanu, E.; Sanduloviciu, M.

2005-01-01

Complex space charge configuration emerges by self-organization in front of an electrode immersed in plasma when its potential is increased at a certain critical value. Consisting from a nucleus protected from the surrounding plasma by an electrical double layer, the complexity reveals an internal structure and behaviour which remind us primitive organisms. Thus the complexity is not static but stationary open system in which continuous decay is constantly compensated by substance and energy from the surrounding plasma. Endowed with a special kind of memory the complexity can work as an intelligent multifunctional system and consequently it is also able to perform innovations after selective interaction with an environment in evolution. Additionally, the complexity is able to replicate by division. (authors)

FEATURES IN THE IMPLEMENTATION MATRIX ORGANIZATIONAL STRUCTURE IN PUBLIC ORGANIZATIONS IN ROMANIA

OpenAIRE

Phd Student Laurentiu BARCAN

2009-01-01

The organization involves the regulated structure of roles that employees have to carry out. The structure is regulated in the sense that all the tasks necessary to achieve the goals are shared, and it is hoped that the award was made to people who can carry out the best. Structure is a management tool and not an end in itself. Its purpose is to help create a framework for human performance. Although the structure should be defined to cover the duties, roles should be designed in light of est...

Persistence of urban organic aerosols composition: Decoding their structural complexity and seasonal variability.

Science.gov (United States)

Matos, João T V; Duarte, Regina M B O; Lopes, Sónia P; Silva, Artur M S; Duarte, Armando C

2017-12-01

Organic Aerosols (OAs) are typically defined as highly complex matrices whose composition changes in time and space. Focusing on time vector, this work uses two-dimensional nuclear magnetic resonance (2D NMR) techniques to examine the structural features of water-soluble (WSOM) and alkaline-soluble organic matter (ASOM) sequentially extracted from fine atmospheric aerosols collected in an urban setting during cold and warm seasons. This study reveals molecular signatures not previously decoded in NMR-related studies of OAs as meaningful source markers. Although the ASOM is less hydrophilic and structurally diverse than its WSOM counterpart, both fractions feature a core with heteroatom-rich branched aliphatics from both primary (natural and anthropogenic) and secondary origin, aromatic secondary organics originated from anthropogenic aromatic precursors, as well as primary saccharides and amino sugar derivatives from biogenic emissions. These common structures represent those 2D NMR spectral signatures that are present in both seasons and can thus be seen as an "annual background" profile of the structural composition of OAs at the urban location. Lignin-derived structures, nitroaromatics, disaccharides, and anhydrosaccharides signatures were also identified in the WSOM samples only from periods identified as smoke impacted, which reflects the influence of biomass-burning sources. The NMR dataset on the H-C molecules backbone was also used to propose a semi-quantitative structural model of urban WSOM, which will aid efforts for more realistic studies relating the chemical properties of OAs with their atmospheric behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Low-Dimensional Organic-Inorganic Halide Perovskite: Structure, Properties, and Applications.

Science.gov (United States)

Misra, Ravi K; Cohen, Bat-El; Iagher, Lior; Etgar, Lioz

2017-10-09

Three-dimensional (3 D) perovskite has attracted a lot of attention owing to its success in photovoltaic (PV) solar cells. However, one of its major crucial issues lies in its stability, which has limited its commercialization. An important property of organic-inorganic perovskite is the possibility of forming a layered material by using long organic cations that do not fit into the octahedral cage. These long organic cations act as a "barrier" that "caps" 3 D perovskite to form the layered material. Controlling the number of perovskite layers could provide a confined structure with chemical and physical properties that are different from those of 3 D perovskite. This opens up a whole new batch of interesting materials with huge potential for optoelectronic applications. This Minireview presents the synthesis, properties, and structural orientation of low-dimensional perovskite. It also discusses the progress of low-dimensional perovskite in PV solar cells, which, to date, have performance comparable to that of 3 D perovskite but with enhanced stability. Finally, the use of low-dimensional perovskite in light-emitting diodes (LEDs) and photodetectors is discussed. The low-dimensional perovskites are promising candidates for LED devices, mainly because of their high radiative recombination as a result of the confined low-dimensional quantum well. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling the Structure and Effectiveness of Intelligence Organizations: Dynamic Information Flow Simulation

National Research Council Canada - National Science Library

Behrman, Robert; Carley, Kathleen

2003-01-01

This paper describes the Dynamic Information Flow Simulation (DIFS), an abstract model for analyzing the structure and function of intelligence support organizations and the activities of entities within...

Structure-Property of Metal Organic Frameworks Calcium Terephthalates Anodes for Lithium-ion Batteries

International Nuclear Information System (INIS)

Wang, Liping; Mou, Chengxu; Sun, Yang; Liu, Wei; Deng, Qijiu; Li, Jingze

2015-01-01

Graphical Abstract: Effects of hydration water in calcium terephthalates anodes on the structure, operational voltage and electrochemical performance are systematically studied. Display Omitted -- Highlights: •Metal organic frameworks CaC 8 H 4 O 4 ·3H 2 O and CaC 8 H 4 O 4 are applied as anodes for lithium ion batteries. •Appearance of hydration water leads different crystallography structures and electrochemical performance. •Anhydrous CaC 8 H 4 O 4 has a spacious ordered layer structure, a higher Ca-O chemical bonding interaction and a higher transparent lithium ion diffusion coefficient, delivering a higher capacity, better cycling performance and rate performance than CaC 8 H 4 O 4 ·3H 2 O. -- Abstract: Metal organic frameworks have attracted considerable interest as electrode materials for lithium ion batteries. In this paper, the metal organic frameworks hydrated calcium terephthalate (CaC 8 H 4 O 4 ·3H 2 O) and anhydrous calcium terephthalate (CaC 8 H 4 O 4 ) as anodes for lithium ion batteries are comparatively studied. Crystallography and local chemical bond analysis are combined to interpret the structure-property of calcium terephthalates. Results show that the anhydrous CaC 8 H 4 O 4 has a spacious ordered layer structure and a higher Ca-O chemical bonding interaction, delivering a higher capacity, better cycling performance and rate performance than CaC 8 H 4 O 4 ·3H 2 O

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

Science.gov (United States)

Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

2016-01-01

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

Directory of Open Access Journals (Sweden)

Laura Delgado-Balbuena

Full Text Available Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826 accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485 inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100% > earthworms applied (92% > organic material applied (77% > untreated soil (57% > surfactant applied (34% after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil

Structural and functional organization of growing tips of Neurospora crassa Hyphae.

Science.gov (United States)

Potapova, T V

2014-07-01

Data are presented on a variety of intracellular structures of the vegetative hyphae of the filamentous fungus Neurospora crassa and the involvement of these structures in the tip growth of the hyphae. Current ideas on the molecular and genetic mechanisms of tip growth and regulation of this process are considered. On the basis of comparison of data on behaviors of mitochondria and microtubules and data on the electrical heterogeneity of the hyphal apex, a hypothesis is proposed about a possible supervisory role of the longitudinal electric field in the structural and functional organization of growing tips of the N. crassa hyphae.

Structural Design Principle of Small-Molecule Organic Semiconductors for Metal-Free, Visible-Light-Promoted Photocatalysis.

Science.gov (United States)

Wang, Lei; Huang, Wei; Li, Run; Gehrig, Dominik; Blom, Paul W M; Landfester, Katharina; Zhang, Kai A I

2016-08-08

Herein, we report on the structural design principle of small-molecule organic semiconductors as metal-free, pure organic and visible light-active photocatalysts. Two series of electron-donor and acceptor-type organic semiconductor molecules were synthesized to meet crucial requirements, such as 1) absorption range in the visible region, 2) sufficient photoredox potential, and 3) long lifetime of photogenerated excitons. The photocatalytic activity was demonstrated in the intermolecular C-H functionalization of electron-rich heteroaromates with malonate derivatives. A mechanistic study of the light-induced electron transport between the organic photocatalyst, substrate, and the sacrificial agent are described. With their tunable absorption range and defined energy-band structure, the small-molecule organic semiconductors could offer a new class of metal-free and visible light-active photocatalysts for chemical reactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interface properties of Fe/MgO/Cu-phthalocyanine metal-insulator-organic semiconductor structures

International Nuclear Information System (INIS)

Lee, Nyunjong; Bae, Yujeong; Kim, Taehee; Ito, Eisuke; Hara, Masahiko

2014-01-01

Hybrid interface structures consisting of organic copper-phthalocyanine (CuPc) and ferromagnetic metal Fe(001) with and without a MgO(001) cover were investigated by using surface sensitive techniques of X-ray photoemission spectroscopy and ultraviolet photoemission spectroscopy. A systematic study of the energy level alignment at the interfaces was carried out. For the hybrid interfaces considered here, our results indicate that the insertion of an artificially-grown ultra-thin oxide layer MgO(001) can prevent Femi level pinning and induce a rather large interface dipole, thereby resulting in remarkable CuPc Fermi level shifts when the thickness of the CuPc film is less than 3 nm. This study provides a better understanding of spin filtering in MgO-based organic spin devices and a new way to alter the interface electronic structure of metal/organic semiconductor hybrid systems.

The Method for Investigating the Structurization of Water-Organic Mixtures

International Nuclear Information System (INIS)

Karitskaya, S

2013-01-01

The investigation of the properties of micellar systems is of great practical importance, since the microheterogeneous structure, in particular, of aqueous-organic solutions can be used to create reaction centers with designed properties, which will make it possible to increase the efficiency of processes associated with the intramolecular conversion of the electronic excitation energy of a molecule. In the present paper, model systems to stimulate chemical reactions are the spatial-temporal structures (STS) formed as a result of photophysical and photochemical reactions, whose time characteristics are highly sensitive to a change in the solvent compositions. The STS evolution processes are slow and the structures formed have macroscopic sizes, which makes the system under consideration a convenient object for experimental studies. The spectral and time characteristics of the spatial-temporal structures luminescing when exposed to UV radiation in aqueous alcohol solutions of anthraquinone are investigated experimentally depending on the volume content of alcohol in a mixture. It is shown that the microheterogeneous structure of aqueous alcohol solutions considerably influences the behavior of the dissipative structures formed

Controlling the dynamics of a self-organized structure using a rf-field

International Nuclear Information System (INIS)

Talasman, S.J.; Ignat, M.

2004-01-01

We investigate the influence of an external rf-field upon a plasma self-organized structure. We show that depending on the intensity of this field, though it is at very low values, the dynamics of the structure can be easily controlled over a wide range of the state parameters values. This could be considered as a non-feedback method of dynamics control

Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting.

Science.gov (United States)

Chen, Yuxiang; Zhang, Yufen; Zhang, Quanguo; Xu, Lixin; Li, Ran; Luo, Xiaopei; Zhang, Xin; Tong, Jin

2015-11-01

In the present study, maize stover was vermicomposted with the epigeic earthworm Eisenia fetida. The results showed that, during vermicomposting process, the earthworms promoted decomposition of maize stover. Analysis of microbial communities of the vermicompost by high-throughput pyrosequencing showed more complex bacterial community structure in the substrate treated by the earthworms than that in the control group. The dominant microbial genera in the treatment with the earthworms were Pseudoxanthomonas, Pseudomonas, Arthrobacter, Streptomyces, Cryptococcus, Guehomyces, and Mucor. Compared to the control group, the relative abundance of lignocellulose degradation microorganisms increased. The results indicated that the earthworms modified the structure of microbial communities during vermicomposting process, activated the growth of lignocellulose degradation microorganisms, and triggered the lignocellulose decomposition.

Chemical evaluation of soil organic matter structure in diverse cropping systems

Science.gov (United States)

Soil organic matter (SOM) improves soil structure, nutrient and water retention, and biodiversity while reducing susceptibility to soil erosion. SOM also represents an important pool of C that can be increased to help mitigate global climate change. Our understanding of how agricultural management ...

Investigating the role for adaptation of the microbial community to transform trace organic chemicals during managed aquifer recharge

KAUST Repository

Alidina, Mazahirali

2014-06-01

This study was undertaken to investigate whether adaptation by pre-exposure to trace organic chemicals (TOrCs) was necessary for microbial transformation during managed aquifer recharge (MAR). Two pairs of laboratory-scale soil columns, each receiving a different primary substrate, were utilized to simulate the dominant bulk organic carbon present in MAR systems receiving wastewater effluent of varying quality and having undergone different degrees of pre-treatment, as well as organic carbon prevalent at different stages of subsurface travel. Each pair of columns consisted of duplicate set-ups receiving the same feed solution with only one pre-exposed to a suite of eight TOrCs for approximately ten months. Following the pre-exposure period, a spiking experiment was conducted in which the non-exposed columns also received the same suite of TOrCs. TOrC attenuation was quantified for the pre- and non-exposed columns of each pair during the spiking experiment. The microbial community structure and function of these systems were characterized by pyrosequencing of 16S rRNA gene and metagenomics, respectively. Biotransformation rather than sorption was identified as the dominant removal mechanism for almost all the TOrCs (except triclocarban). Similar removal efficiencies were observed between pre-exposed and non-exposed columns for most TOrCs. No obvious differences in microbial community structure were revealed between pre- and non-exposed columns. Using metagenomics, biotransformation capacity potentials of the microbial community present were also similar between pre- and non-exposed columns of each pair. Overall, the pre-exposure of MAR systems to TOrCs at ng/L levels did not affect their attenuation and had no obvious influence on the resulting microbial community structure and function. Thus, other factors such as bioavailability of the primary substrate play a greater role regarding biotransformation of TOrCs. These results indicate that MAR systems adapted to a

Investigating the role for adaptation of the microbial community to transform trace organic chemicals during managed aquifer recharge.

Science.gov (United States)

Alidina, Mazahirali; Li, Dong; Drewes, Jörg E

2014-06-01

This study was undertaken to investigate whether adaptation by pre-exposure to trace organic chemicals (TOrCs) was necessary for microbial transformation during managed aquifer recharge (MAR). Two pairs of laboratory-scale soil columns, each receiving a different primary substrate, were utilized to simulate the dominant bulk organic carbon present in MAR systems receiving wastewater effluent of varying quality and having undergone different degrees of pre-treatment, as well as organic carbon prevalent at different stages of subsurface travel. Each pair of columns consisted of duplicate set-ups receiving the same feed solution with only one pre-exposed to a suite of eight TOrCs for approximately ten months. Following the pre-exposure period, a spiking experiment was conducted in which the non-exposed columns also received the same suite of TOrCs. TOrC attenuation was quantified for the pre- and non-exposed columns of each pair during the spiking experiment. The microbial community structure and function of these systems were characterized by pyrosequencing of 16S rRNA gene and metagenomics, respectively. Biotransformation rather than sorption was identified as the dominant removal mechanism for almost all the TOrCs (except triclocarban). Similar removal efficiencies were observed between pre-exposed and non-exposed columns for most TOrCs. No obvious differences in microbial community structure were revealed between pre- and non-exposed columns. Using metagenomics, biotransformation capacity potentials of the microbial community present were also similar between pre- and non-exposed columns of each pair. Overall, the pre-exposure of MAR systems to TOrCs at ng/L levels did not affect their attenuation and had no obvious influence on the resulting microbial community structure and function. Thus, other factors such as bioavailability of the primary substrate play a greater role regarding biotransformation of TOrCs. These results indicate that MAR systems adapted to a

Organization structure. Main activities of the Division

International Nuclear Information System (INIS)

2008-01-01

In this chapter the organization structure as well as main activities of the Division for radiation safety, NPP decommissioning and radioactive waste management are presented. This Division of the VUJE, a.s. consists of the following sections and departments: Section for economic and technical services; Section for radiation protection of employees; Department for management of emergency situations and risk assessment; Department for implementation of nuclear power facilities decommissioning and RAW management; Department for personnel and environmental dosimetry; Department for preparation of NPP decommissioning; Department for RAW treatment technologies; Department for chemical regimes and physico-chemical analyses; Department for management of nuclear power facilities decommissioning and RAW management. Main activities of this Division are presented.

Electronic Structure Approach to Tunable Electronic Properties of Hybrid Organic-Inorganic Perovskites

Science.gov (United States)

Liu, Garnett; Huhn, William; Mitzi, David B.; Kanai, Yosuke; Blum, Volker

We present a study of the electronic structure of layered hybrid organic-inorganic perovskite (HOIP) materials using all-electron density-functional theory. Varying the nature of the organic and inorganic layers should enable systematically fine-tuning the carrier properties of each component. Using the HSE06 hybrid density functional including spin-orbit coupling (SOC), we validate the principle of tuning subsystem-specific parts of the electron band structures and densities of states in CH3NH3PbX3 (X=Cl, Br, I) compared to a modified organic component in layered (C6H5C2H4NH3) 2PbX4 (X=Cl, Br, I) and C20H22S4N2PbX4 (X=Cl, Br, I). We show that tunable shifts of electronic levels indeed arise by varying Cl, Br, I as the inorganic components, and CH3NH3+ , C6H5C2H4NH3+ , C20H22S4N22 + as the organic components. SOC is found to play an important role in splitting the conduction bands of the HOIP compounds investigated here. The frontier orbitals of the halide shift, increasing the gap, when Cl is substituted for Br and I.

Hybrid Organic-Inorganic Perovskites: Structural Diversity and Opportunities for Semiconductor Design

Science.gov (United States)

Mitzi, David

Photovoltaic (PV) devices based on three-dimensional perovskites, (Cs, MA, FA)Pb(I, Br)3 (MA =methylammonium, FA =formamidinium), have attracted substantial recent interest, because of the unprecedented rise in power conversion efficiency to values above 20%, which in turn is made possible by the near ideal band gap, strong optical absorption, high carrier mobilities, long minority carrier lifetimes, and relatively benign defects and grain boundaries for the absorbers. Some of the same properties that render these materials near-ideal for PV, also make them attractive for LED and other optoelectronic applications. Despite the high levels of device performance, the incorporation of the heavy metal lead, coupled with issues of device stability and electrical hysteresis pose challenges for commercializing these exciting technologies. This talk will provide a perspective on and discuss recent advances related to the broader perovskite family, focusing on the extraordinary structural/chemical diversity, including ability to control structural/electronic dimensionality, substitute on the organic cation, metal or halogen sites, and prospects of multi-functionality arising from separately engineered organic/inorganic structural components (e.g., see). Further exploration within this perovskite structural and chemical space offers exciting opportunities for future energy and electronic materials design. This work has been financially supported by the Office of Energy Efficiency and Renewable Energy (EERE), U.S. Dept. of Energy, under Award Number DE-EE0006712.

Inorganic Biominerals in Crustaceans are Structurally Independent of Organic Framework

Science.gov (United States)

Mergelsberg, S. T.; Michel, F. M.; Mukhopadhyay, B.; Dove, P. M.

2015-12-01

Biomineralization of calcium carbonate (CaCO3) as crystalline calcite or amorphous CaCO3 (ACC) occurs in the exoskeletons of all crustaceans. These cuticles are complex composites of inorganic mineral and organic macromolecules with highly divergent morphologies that are adapted to the extreme variations in environmental pressures within their diverse ecological niches. The remarkable variations and adaptations that form, infer a highly efficient and regulated mechanism for biomineralization that is most likely orchestrated by a myriad of biomacromolecules (Ziegler A 2012). The roles of these peptides and organic metabolites during CaCO3 biomineralization are not well understood. In part, this is due to a lack of knowledge of crustacean homeostasis. In a step toward understanding cuticle mineralization in crustaceans, this study asks: Which molecules affect biomineralization? Do the biomineral-active molecules vary greatly between species and body parts? Recent studies of polysaccharide controls on mineralization also raise the question of whether small heterogeneities in chitin, the most abundant biopolymer of the composite, could be primarily responsible for differences in CaCO3 crystallinity. This study used a novel spectroscopic approach to characterize the mineral and organic components of exoskeletons from three Malacostraca organisms — American Lobster (Homarus americanus), Dungeness Crab (Metacarcinus magister), and Red Rock Crab (Cancer productus). Using high-energy x-ray diffraction and Raman spectroscopy, the cuticles of three major body parts from these organisms were analyzed for the structure and bulk chemistry of its chitin and CaCO3 components. The findings indicate that Raman spectroscopy provides adequate resolution to show that crystallinity of chitin and the CaCO3 mineral component are chemically independent of each other, although their crystallinities co-vary for Brachyura species (Dungeness and Red Rock Crabs). Insights from this study

An Improved Conceptually-Based Method for Analysis of Communication Network Structure of Large Complex Organizations.

Science.gov (United States)

Richards, William D., Jr.

Previous methods for determining the communication structure of organizations work well for small or simple organizations, but are either inadequate or unwieldy for use with large complex organizations. An improved method uses a number of different measures and a series of successive approximations to order the communication matrix such that…

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

Science.gov (United States)

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Do differences in food web structure between organic and conventional farms affect the ecosystem service of pest control?

Science.gov (United States)

Macfadyen, Sarina; Gibson, Rachel; Polaszek, Andrew; Morris, Rebecca J; Craze, Paul G; Planqué, Robert; Symondson, William O C; Memmott, Jane

2009-03-01

While many studies have demonstrated that organic farms support greater levels of biodiversity, it is not known whether this translates into better provision of ecosystem services. Here we use a food-web approach to analyse the community structure and function at the whole-farm scale. Quantitative food webs from 10 replicate pairs of organic and conventional farms showed that organic farms have significantly more species at three trophic levels (plant, herbivore and parasitoid) and significantly different network structure. Herbivores on organic farms were attacked by more parasitoid species on organic farms than on conventional farms. However, differences in network structure did not translate into differences in robustness to simulated species loss and we found no difference in percentage parasitism (natural pest control) across a variety of host species. Furthermore, a manipulative field experiment demonstrated that the higher species richness of parasitoids on the organic farms did not increase mortality of a novel herbivore used to bioassay ecosystem service. The explanation for these differences is likely to include inherent differences in management strategies and landscape structure between the two farming systems.

Design guideline for Si/organic hybrid solar cell with interdigitated back contact structure

Science.gov (United States)

Bimo Prakoso, Ari; Rusli; Li, Zeyu; Lu, Chenjin; Jiang, Changyun

2018-03-01

We study the design of Si/organic hybrid (SOH) solar cells with interdigitated back contact (IBC) structure. SOH solar cells formed between n-Si and poly(3,4-ethylenedioxythiophene): polystyrenesulphonate (PEDOT:PSS) is a promising concept that combines the excellent electronic properties of Si with the solution-based processing advantage of an organic polymer. The IBC cell structure is employed to minimize parasitic absorption losses in the organic polymer, eliminate grid shadowing losses, and allow excellent passivation of the front Si surface in one step over a large area. The influence of Si thickness, doping concentration and contact geometry are simulated in this study to optimize the performance of the SOH-IBC solar cell. We found that a high power conversion efficiency of >20% can be achieved for optimized SOH-IBC cell based on a thin c-Si substrate of 40 μm thickness.

Laser Control of Self-Organization Process in Microscopic Region and Fabrication of Fine Microporous Structure

OpenAIRE

Matsumura, Yukimasa; Inami, Wataru; Kawata, Yoshimasa

2012-01-01

We present a controlling technique of microporous structure by laser irradiation during self-organization process. Self-organization process is fabrication method of microstructure. Polymer solution was dropped on the substrate at high humid condition. Water in air appears dropping air temperature below the dew point. The honeycomb structure with regularly aligned pores on the film was fabricated by attaching water droplets onto the solution surface. We demonstrate that it was possible to pre...

The Impact of the Demand for Integration in the Large Multi-Business Unit Firm on the IT Organization Structure

Science.gov (United States)

Larson, Eric Christopher

2012-01-01

Large, multi-business unit firms are decentralizing their overall corporate structures. At the same time, the structures of their IT organizations are becoming more centralized. This is contrary to current wisdom that the IT organization structure will mimic the structure of the corporation, all else being equal. Because the general business…

Assessment of bacterial diversity in Hyalomma aegyptium, H. marginatum and H. excavatum ticks through tag-encoded pyrosequencing.

Science.gov (United States)

Keskin, Adem; Bursali, Ahmet; Snow, David E; Dowd, Scot E; Tekin, Saban

2017-12-01

Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia. To the authors' knowledge, this work represents the first detection of Yersinia enterocolitica in the tick H. excavatum, raising questions regarding the vector competency of this tick, as well as associations of different disease representations perhaps through previously unforeseen routes of pathogen introduction. Likewise, similar questions are related to the presence of Legionella pneumophila in one H. excavatum sample.

Insight into the bacterial diversity of fermentation woad dye vats as revealed by PCR-DGGE and pyrosequencing.

Science.gov (United States)

Milanović, Vesna; Osimani, Andrea; Taccari, Manuela; Garofalo, Cristiana; Butta, Alessandro; Clementi, Francesca; Aquilanti, Lucia

2017-07-01

The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.

Structuring the Administrative Organization of Local School Systems. Educational Research Service Circular No. 2.

Science.gov (United States)

American Association of School Administrators, Washington, DC.

This paper is intended to assist school administrators in improving existing school organizations. It discusses the nature of organizations, provides indicators of reorganization timing, and discusses the task of reorganization. A matrix chart, used to analyze and compare different organizational structures, is provided with explanations.…

Perspectives of experimental and theoretical studies of self-organized dust structures in complex plasmas under microgravity conditions

International Nuclear Information System (INIS)

Tsytovich, V N

2015-01-01

We review research aimed at understanding the phenomena occurring in a complex plasma under microgravity conditions. Some aspects of the work already performed are considered that have not previously been given sufficient attention but which are potentially crucial for future work. These aspects, in particular, include the observation of compact dust structures that are estimated to be capable of confining all components of a dust plasma in a bounded spatial volume; experimental evidence of the nonlinear screening of dust particles; and experimental evidence of the excitation of collective electric fields. In theoretical terms, novel collective attraction processes between likely charged dust particles are discussed and all schemes of the shadowy attraction between dust particles used earlier, including in attempts to interpret observations, are reviewed and evaluated. Dust structures are considered from the standpoint of the current self-organization theory. It is emphasized that phase transitions between states of self-organized systems differ significantly from those in homogeneous states and that the phase diagrams should be constructed in terms of the parameters of a self-organized structure and cannot be constructed in terms of the temperature and density or similar parameters of homogeneous structures. Using the existing theoretical approaches to modeling self-organized structures in dust plasmas, the parameter distribution of a structure is recalculated for a simpler model that includes the quasineutrality condition and neglects diffusion. These calculations indicate that under microgravity conditions, any self-organized structure can contain a limited number of dust particles and is finite in size. The maximum possible number of particles in a structure determines the characteristic inter-grain distance in dust crystals that can be created under microgravity conditions. Crystallization criteria for the structures are examined and the quasispherical

Molecular design chemical structure generation from the properties of pure organic compounds

CERN Document Server

Horvath, AL

1992-01-01

This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

Ordered organic-organic multilayer growth

Science.gov (United States)

Forrest, Stephen R; Lunt, Richard R

2015-01-13

An ordered multilayer crystalline organic thin film structure is formed by depositing at least two layers of thin film crystalline organic materials successively wherein the at least two thin film layers are selected to have their surface energies within .+-.50% of each other, and preferably within .+-.15% of each other, whereby every thin film layer within the multilayer crystalline organic thin film structure exhibit a quasi-epitaxial relationship with the adjacent crystalline organic thin film.

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

Science.gov (United States)

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

2014-09-01

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

Structure and organization of heteromeric AMPA-type glutamate receptors.

Science.gov (United States)

Herguedas, Beatriz; García-Nafría, Javier; Cais, Ondrej; Fernández-Leiro, Rafael; Krieger, James; Ho, Hinze; Greger, Ingo H

2016-04-29

AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling. Copyright © 2016, American Association for the Advancement of Science.

Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms

NARCIS (Netherlands)

De Bie, T.; De Meester, L.; Brendonck, L.; Martens, K.; Goddeeris, B.; Ercken, D.; Hampel, H.; Denys, L.; Vanhecke, L.; Van der Gucht, K.; Van Wichelen, J.; Vyverman, W.; Declerck, S.A.J.

2012-01-01

Relationships between traits of organisms and the structure of their metacommunities have so far mainly been explored with meta-analyses. We compared metacommunities of a wide variety of aquatic organism groups (12 groups, ranging from bacteria to fish) in the same set of 99 ponds to minimise biases

Unravelling surface and interfacial structures of a metal–organic framework by transmission electron microscopy

KAUST Repository

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-01-01

.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM

Local Electronic Structure of a Single-Layer Porphyrin-Containing Covalent Organic Framework

KAUST Repository

Chen, Chen; Joshi, Trinity; Li, Huifang; Chavez, Anton D.; Pedramrazi, Zahra; Liu, Pei-Nian; Li, Hong; Dichtel, William R.; Bredas, Jean-Luc; Crommie, Michael F.

2017-01-01

We have characterized the local electronic structure of a porphyrin-containing single-layer covalent organic framework (COF) exhibiting a square lattice. The COF monolayer was obtained by the deposition of 2,5-dimethoxybenzene-1,4-dicarboxaldehyde

Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

KAUST Repository

Li, Haoyuan; Qiu, Yong; Duan, Lian

2016-01-01

A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using

Organization, structure, and performance in the US nuclear power industry

International Nuclear Information System (INIS)

Lester, R.K.

1986-01-01

Several propositions are advanced concerning the effects of industry organization and structure on the economic performance of the American commercial nuclear power industry. Both the electric utility industry and the nuclear power plant supply industry are relatively high degree of horizontal disaggregation. The latter is also characterized by an absence of vertical integration. The impact of each of these factors on construction and operating performance is discussed. Evidence is presented suggesting that the combination of horizontal and vertical disaggregation in the industry has had a significant adverse effect on economic performance. The relationship between industrial structure and regulatory behavior is also discussed. 43 references, 4 figures, 9 tables

Anthraquinone with Tailored Structure for Nonaqueous Metal-Organic Redox Flow Battery

Energy Technology Data Exchange (ETDEWEB)

Wang, Wei; Xu, Wu; Cosimbescu, Lelia; Choi, Daiwon; Li, Liyu; Yang, Zhenguo

2012-06-08

A nonaqueous, hybrid metal-organic redox flow battery based on tailored anthraquinone structure is demonstrated to have an energy efficiency of {approx}82% and a specific discharge energy density similar to aqueous redox flow batteries, which is due to the significantly improved solubility of anthraquinone in supporting electrolytes.

REMOTE WORK AS A PROMISING FORM OF LABOUR ORGANIZATION FOR RUSSIAN ENTREPRENEURIAL STRUCTURES

Directory of Open Access Journals (Sweden)

I. Gurova

2016-01-01

Full Text Available Remote work (telecommuting is one of the modern technologies of the organization of the labor process, which is not yet widely used in domestic practice. However, in times of crisis, when entrepreneurial structures seek for the maximum reduction of expenses, it can be a tool to address many of the pressing issues related to the most effective use of production and labor resources.The article discusses the features of the remote work on a world level and in our country, detected its strengths and weaknesses for the participants of labour relations, as well as revealed the potential of this form of labor organization for achievement of optimum balance between expenses and efficiency of entrepreneurial structures.

Synchrotron-based measurements of the electronic structure of the organic semiconductor copper phthalocyanine

International Nuclear Information System (INIS)

Downes, J.E.

2004-01-01

Full text: Copper phthalocyanine (CuPc) is a prototypical molecular organic semiconductor that is currently used in the construction of many organic electronic devices such as organic light emitting diodes (OLEDs). Although the material is currently being used, and despite many experimental and theoretical studies, it's detailed electronic structure is still not completely understood. This is likely due to two key factors. Firstly, the interaction of the Cu 3d and phthalocyanine ligand 2p electrons leads to the formation of a complex arrangement of localized and delocalized states near the Fermi level. Secondly, thin films of the material are subject to damage by the photon beam used to make measurements of their electronic structure. Using the synchrotron-based techniques of soft x-ray emission spectroscopy (XES) and x-ray photoemission spectroscopy (XPS), we have measured the detailed electronic structure of in-situ grown thin film samples of CuPc. Beam damage was minimized by continuous translation of the sample during data acquisition. The results obtained differ significantly from previous XES and ultraviolet photoemission measurements, but are in excellent agreement with recent density functional calculations. The reasons for these discrepancies will be explained, and their implications for future measurements on similar materials will be explored

Crystal structures of seven molecular salts derived from benzylamine and organic acidic components

Science.gov (United States)

Wen, Xianhong; Jin, Xiunan; Lv, Chengcai; Jin, Shouwen; Zheng, Xiuqing; Liu, Bin; Wang, Daqi; Guo, Ming; Xu, Weiqiang

2017-07-01

Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids gave a total of seven molecular salts with the compositions: (benzylamine): (p-toluenesulfonic acid) (1) [(HL)+ · (tsa-)], (benzylamine): (o-nitrobenzoic acid) (2) [(HL+) · (onba)-], (benzylamine): (3,4-methylenedioxybenzoic acid) (3) [(HL+) · (mdba-)], (benzylamine): (mandelic acid) (4) [(HL+) · (mda-)], (benzylamine): (5-bromosalicylic acid)2(5) [(HL+) · (bsac-) · (Hbsac)], (benzylamine): (m-phthalic acid) (6) [(HL+) · (Hmpta-)], and (benzylamine)2: (trimesic acid) (7) [(HL+)2 · (Htma2-)]. The seven salts have been characterised by X-ray diffraction technique, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the seven investigated crystals the NH2 groups in the benzylamine moieties are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond formation between the ammonium and the deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 4-7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CHsbnd π/CH2sbnd π, Osbnd O, and Osbnd Cπ associations contribute to the stabilization and expansion of the total high-dimensional (2D-3D) framework structures. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R42(8), R43(10) and R44(12), usually observed in organic solids of organic acids with amine, were again shown to be involved in constructing most of these hydrogen bonding networks.

Reconstruction of structure and function in tissue engineering of solid organs: Toward simulation of natural development based on decellularization.

Science.gov (United States)

Zheng, Chen-Xi; Sui, Bing-Dong; Hu, Cheng-Hu; Qiu, Xin-Yu; Zhao, Pan; Jin, Yan

2018-04-27

Failure of solid organs, such as the heart, liver, and kidney, remains a major cause of the world's mortality due to critical shortage of donor organs. Tissue engineering, which uses elements including cells, scaffolds, and growth factors to fabricate functional organs in vitro, is a promising strategy to mitigate the scarcity of transplantable organs. Within recent years, different construction strategies that guide the combination of tissue engineering elements have been applied in solid organ tissue engineering and have achieved much progress. Most attractively, construction strategy based on whole-organ decellularization has become a popular and promising approach, because the overall structure of extracellular matrix can be well preserved. However, despite the preservation of whole structure, the current constructs derived from decellularization-based strategy still perform partial functions of solid organs, due to several challenges, including preservation of functional extracellular matrix structure, implementation of functional recellularization, formation of functional vascular network, and realization of long-term functional integration. This review overviews the status quo of solid organ tissue engineering, including both advances and challenges. We have also put forward a few techniques with potential to solve the challenges, mainly focusing on decellularization-based construction strategy. We propose that the primary concept for constructing tissue-engineered solid organs is fabricating functional organs based on intact structure via simulating the natural development and regeneration processes. Copyright © 2018 John Wiley & Sons, Ltd.

Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

Science.gov (United States)

Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

2012-01-01

This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

Full color organic light-emitting devices with microcavity structure and color filter.

Science.gov (United States)

Zhang, Weiwei; Liu, Hongyu; Sun, Runguang

2009-05-11

This letter demonstrated the fabrication of the full color passive matrix organic light-emitting devices based on the combination of the microcavity structure, color filter and a common white polymeric OLED. In the microcavity structure, patterned ITO terraces with different thickness were used as the anode as well as cavity spacer. The primary color emitting peaks were originally generated by the microcavity and then the second resonance peak was absorbed by the color filter.

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

Directory of Open Access Journals (Sweden)

David Correa-Galeote

2016-07-01

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

Organic chemistry as a language and the implications of chemical linguistics for structural and retrosynthetic analyses.

Science.gov (United States)

Cadeddu, Andrea; Wylie, Elizabeth K; Jurczak, Janusz; Wampler-Doty, Matthew; Grzybowski, Bartosz A

2014-07-28

Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics-based analysis appears well-suited to the analysis of complex structural and reactivity patterns within organic molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution of Organic Agriculture within Theoretical Frameworks of Structural Change and Transformation

DEFF Research Database (Denmark)

Rasmussen, Ole Horn

with the idea of organic agriculture, agricultural structural change and transformation. However, the search for an answer to the research question starts with a contribution with a fragmentary status. Marshall and the theory of externalities present a deepen of the Danish agricultural economists...... it is possibly to draw a link to our initially discussion about definition of organic agriculture. The principles between conventional and organic agriculture differ. We have two kinds of rationalities. Exactly such approach is the methodological hard core in the works of Chayanov and we link to a tentative...... suggestion for working towards, as a minimum, a double definition of organic agriculture. The last "agricultural economist" is Hvelplund. Despite his position as a researcher within energy, we have different arguments for our presentation of him here. The first argument is that Hvelplund is occupied...

Chemical-Structural Changes of Organic Matter in a Semi-Arid Soil After Organic Amendment

Institute of Scientific and Technical Information of China (English)

C.NICOL(A)S; G.MASCIANDARO; T.HERN(A)NDEZ; C.GARCIA

2012-01-01

A 9-month incubation experiment using composted and non-composted amendments derived from vine pruning waste and sewage sludge was carried out to study the effects of the nature and stability of organic amendments on the structural composition of organic matter (OM) in a semi-arid soil. The changes of soil OM,both in the whole soil and in the extractable carbon with pyrophosphate,were evaluated by pyrolysis-gas chromatography and chemical analyses.By the end of the experiment,the soils amended with pruning waste exhibited less organic carbon loss than those receiving sewage sludge.The non-composted residues increased the aliphatic-pyrolytic products of the OM,both in the whole soil and also in the pyrophosphate extract,with the products derived from peptides and proteins being significantly higher.After 9 months,in the soils amended with pruning waste the relative abundance of phenolic-pyrolytic products derived from phenolic compounds,lignin and proteins in the whole soil tended to increase more than those in the soils amended with sewage sludge.However,the extractable OM with pyrophosphate in the soils amended with composted residues tended to have higher contents of these phenolic-pyrolytic products than that in non-composted ones.Thus,despite the stability of pruning waste,the composting of this material promoted the incorporation of phenolic compounds to the soil OM.The pyrolytic indices (furfural/pyrrole and aliphatic/aromatic ratios) showed the diminution of aliphatic compounds and the increase of aromatic compounds,indicating the stabilization of the OM in the amended soils after 9 months.In conclusion,the changes of soil OM depend on the nature and stability of the organic amendments,with composted vine pruning waste favouring humification.

Effects of organic enrichment on macrofauna community structure: an experimental approach

Directory of Open Access Journals (Sweden)

Rodrigo Riera

2013-12-01

Full Text Available The determination of the resilience of benthic assemblages is a capital issue for the off-shore aquaculture industry in its attempts to minimize environmental disturbances. Experimental studies are an important tool for the establishment of thresholds for macrofaunal assemblages inhabiting sandy seabeds. An experiment was conducted with three treatments (Control, 1x and 3x,in which organic load (fish pellets was added (1x (10 g of fish pellets and 3x (30 g. A reduction in abundance of individuals and species richness was found as between the control and organic-enriched treatments. Significant changes in assemblage structure were also found, mainly due to the decrease of the sensitive tanaid Apseudes talpa in organically-enriched treatments. AMBI and M-AMBI indices were calculated and a decrease of ecological status was observed in treatment 3x.

Modern electronic structure theory and applications in organic chemistry

CERN Document Server

Davidson, ER

1997-01-01

This volume focuses on the use of quantum theory to understand and explain experiments in organic chemistry. High level ab initio calculations, when properly performed, are useful in making quantitative distinctions between various possible interpretations of structures, reactions and spectra. Chemical reasoning based on simpler quantum models is, however, essential to enumerating the likely possibilities. The simpler models also often suggest the type of wave function likely to be involved in ground and excited states at various points along reaction paths. This preliminary understanding is n

Performances of two biotrickling filters in treating H₂S-containing waste gases and analysis of corresponding bacterial communities by pyrosequencing.

Science.gov (United States)

Li, Jianjun; Ye, Guangyun; Sun, Duanfang; Sun, Guoping; Zeng, Xiaowei; Xu, Jian; Liang, Shizhong

2012-09-01

Two identical biotrickling filters named BTFa and BTFb were run in parallel to examine their performances in removing hydrogen sulfide. BTFa was filled with ceramic granules, and BTFb was filled with volcanic rocks. The results showed that BTFb was more robust than BTFa under acidic conditions. At empty bed residence times (EBRTs) of 20 and 15 s, the removal efficiency of BTFa was close to 100%. At EBRTs of 10 and 5 s, the removal efficiency of BTFa slightly decreased. The removal efficiencies of BTFa decreased by different degrees at the end of each stage, dropping to 94%, 81%, 60%, and 71%, respectively. However, the H(2)S removal efficiency in BTFb consistently reached 99% throughout the experiment. Pyrosequencing analyses indicated that members of Thiomonas dominated in both BTFs, but the relative abundance of Acidithiobacillus was higher in BTFb than in BTFa.

Resolving anatomical and functional structure in human brain organization: identifying mesoscale organization in weighted network representations.

Science.gov (United States)

Lohse, Christian; Bassett, Danielle S; Lim, Kelvin O; Carlson, Jean M

2014-10-01

Human brain anatomy and function display a combination of modular and hierarchical organization, suggesting the importance of both cohesive structures and variable resolutions in the facilitation of healthy cognitive processes. However, tools to simultaneously probe these features of brain architecture require further development. We propose and apply a set of methods to extract cohesive structures in network representations of brain connectivity using multi-resolution techniques. We employ a combination of soft thresholding, windowed thresholding, and resolution in community detection, that enable us to identify and isolate structures associated with different weights. One such mesoscale structure is bipartivity, which quantifies the extent to which the brain is divided into two partitions with high connectivity between partitions and low connectivity within partitions. A second, complementary mesoscale structure is modularity, which quantifies the extent to which the brain is divided into multiple communities with strong connectivity within each community and weak connectivity between communities. Our methods lead to multi-resolution curves of these network diagnostics over a range of spatial, geometric, and structural scales. For statistical comparison, we contrast our results with those obtained for several benchmark null models. Our work demonstrates that multi-resolution diagnostic curves capture complex organizational profiles in weighted graphs. We apply these methods to the identification of resolution-specific characteristics of healthy weighted graph architecture and altered connectivity profiles in psychiatric disease.

De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

Directory of Open Access Journals (Sweden)

Parani Madasamy

2011-04-01

Full Text Available Abstract Background Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas. Results From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis. Conclusion The large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil

De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.

Science.gov (United States)

Natarajan, Purushothaman; Parani, Madasamy

2011-04-15

Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas. From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis. The large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of

Adjustable threshold-voltage in all-inkjet-printed organic thin film transistor using double-layer dielectric structures

International Nuclear Information System (INIS)

Wu, Wen-Jong; Lee, Chang-Hung; Hsu, Chun-Hao; Yang, Shih-Hsien; Lin, Chih-Ting

2013-01-01

An all-inkjet-printed organic thin film transistor (OTFT) with a double-layer dielectric structure is proposed and implemented in this study. By using the double-layer structure with different dielectric materials (i.e., polyvinylphenol with poly(vinylidene fluoride-co-hexafluoropropylene)), the threshold-voltage of OTFT can be adjusted. The threshold-voltage shift can be controlled by changing the composition of dielectric layers. That is, an enhancement-mode OTFT can be converted to a depletion-mode OTFT by selectively printing additional dielectric layers to form a high-k/low-k double-layer structure. The printed OTFT has a carrier mobility of 5.0 × 10 −3 cm 2 /V-s. The threshold-voltages of the OTFTs ranged between − 13 V and 10 V. This study demonstrates an additional design parameter for organic electronics manufactured using inkjet printing technology. - Highlights: • A double-layer dielectric organic thin film transistor, OTFT, is implemented. • The threshold voltage of OTFT can be configured by the double dielectric structure. • The composition of the dielectric determines the threshold voltage shift. • The characteristics of OTFTs can be adjusted by double dielectric structures

In situ KPFM imaging of local photovoltaic characteristics of structured organic photovoltaic devices.

Science.gov (United States)

Watanabe, Satoshi; Fukuchi, Yasumasa; Fukasawa, Masako; Sassa, Takafumi; Kimoto, Atsushi; Tajima, Yusuke; Uchiyama, Masanobu; Yamashita, Takashi; Matsumoto, Mutsuyoshi; Aoyama, Tetsuya

2014-02-12

Here, we discuss the local photovoltaic characteristics of a structured bulk heterojunction, organic photovoltaic devices fabricated with a liquid carbazole, and a fullerene derivative based on analysis by scanning kelvin probe force microscopy (KPFM). Periodic photopolymerization induced by an interference pattern from two laser beams formed surface relief gratings (SRG) in the structured films. The surface potential distribution in the SRGs indicates the formation of donor and acceptor spatial distribution. Under illumination, the surface potential reversibly changed because of the generation of fullerene anions and hole transport from the films to substrates, which indicates that we successfully imaged the local photovoltaic characteristics of the structured photovoltaic devices. Using atomic force microscopy, we confirmed the formation of the SRG because of the material migration to the photopolymerized region of the films, which was induced by light exposure through photomasks. The structuring technique allows for the direct fabrication and the control of donor and acceptor spatial distribution in organic photonic and electronic devices with minimized material consumption. This in situ KPFM technique is indispensable to the fabrication of nanoscale electron donor and electron acceptor spatial distribution in the devices.

Forest products research and development organizations in a worldwide setting: A review of structure, governance, and measures of performance of organizations outside the United States

Science.gov (United States)

Paul V. Ellefson; Michael A. Kilgore; Kenneth E. Skog; Christopher D. Risbrudt

2007-01-01

Located in 23 countries, 40 forest-products research and development organizations outside the United States were reviewed in 2004 and 2005. The intent was to obtain a better understanding of how such organizations are structured and administered and their performance judged. Investing over $600 million annually, the 40 organizations employed 7,000 to 7,500 scientists...

Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar (Coleoptera: Curculionidae Reveals Multiple Protease-Like Transcripts.

Directory of Open Access Journals (Sweden)

Arnubio Valencia

Full Text Available The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts.

Science.gov (United States)

Valencia, Arnubio; Wang, Haichuan; Soto, Alberto; Aristizabal, Manuel; Arboleda, Jorge W; Eyun, Seong-Il; Noriega, Daniel D; Siegfried, Blair

2016-01-01

The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.

Electronic structure of self-organized InAs/GaAs quantum dots bounded by {136} facets

International Nuclear Information System (INIS)

Yang, Weidong; Lee, Hao; Johnson, Thomas J.; Sercel, Peter C.; Norman, A. G.

2000-01-01

Recent experiments indicate that the shape of self-organized InAs quantum dots grown on GaAs [001] is an elongated pyramid with bounding facets corresponding to a family of four {136} planes. This structure, which possesses C 2v symmetry, is quite different from square-base pyramidal or lens geometries, which have been assumed in previous electronic structure calculations for this system. In this paper, we consider theoretically the influence of the {136} shape on the electronic structure and optical properties of the quantum dots. We present a valence force-field calculation of the inhomogeneous strain and incorporate the results into an eight band k(vector sign)·p(vector sign) electronic structure calculation. The size dependence of the electronic structure is calculated and compared to experimental photoluminescence spectra. The effects of perturbations on the {136} shape are also considered. Calculations based on the {136} shape give good agreement with the observed level structure and optical polarization properties of self-organized InAs/GaAs quantum dots. (c) 2000 The American Physical Society

Using Structure-Based Organic Chemistry Online Tutorials with Automated Correction for Student Practice and Review

Science.gov (United States)

O'Sullivan, Timothy P.; Hargaden, Gra´inne C.

2014-01-01

This article describes the development and implementation of an open-access organic chemistry question bank for online tutorials and assessments at University College Cork and Dublin Institute of Technology. SOCOT (structure-based organic chemistry online tutorials) may be used to supplement traditional small-group tutorials, thereby allowing…

Unique vaginal microbiota that includes an unknown Mycoplasma-like organism is associated with Trichomonas vaginalis infection.

Science.gov (United States)

Martin, David H; Zozaya, Marcela; Lillis, Rebecca A; Myers, Leann; Nsuami, M Jacques; Ferris, Michael J

2013-06-15

The prevalence of Trichomonas vaginalis infection is highest in women with intermediate Nugent scores. We hypothesized that the vaginal microbiota in T. vaginalis-infected women differs from that in T. vaginalis-uninfected women. Vaginal samples from 30 T. vaginalis-infected women were matched by Nugent score to those from 30 T. vaginalis-uninfected women. Equal numbers of women with Nugent scores categorized as normal, intermediate, and bacterial vaginosis were included. The vaginal microbiota was assessed using 454 pyrosequencing analysis of polymerase chain reaction-amplified 16S ribosomal RNA gene sequences. The 16S ribosomal RNA gene sequence of an unknown organism was obtained by universal bacterial polymerase chain reaction amplification, cloning, and sequencing. Principal coordinates analysis of the pyrosequencing data showed divergence of the vaginal microbiota in T. vaginalis-infected and T. vaginalis-uninfected patients among women with normal and those with intermediate Nugent scores but not among women with bacterial vaginosis. Cluster analysis revealed 2 unique groups of T. vaginalis-infected women. One had high abundance of Mycoplasma hominis and other had high abundance of an unknown Mycoplasma species. Women in the former group had clinical evidence of enhanced vaginal inflammation. T. vaginalis may alter the vaginal microbiota in a manner that is favorable to its survival and/or transmissibility. An unknown Mycoplasma species plays a role in some of these transformations. In other cases, these changes may result in a heightened host inflammatory response.

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

Science.gov (United States)

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Structural changes of organic solids caused by irradiation: raman study at very low temperatures

International Nuclear Information System (INIS)

Hase, Hirotomo; Ishioka, Kunie; Miyatake, Yoko.

1995-01-01

In this paper we first describe a simple liquid helium cryostat and a device of making and mounting organic solid samples. We then present the Raman spectra for irradiated ethanol crystal that were obtained by using the new cryostat and demonstrate how the Raman method is useful for getting insight into structural changes of organic solids caused by irradiation. (J.P.N.)

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

Directory of Open Access Journals (Sweden)

Veronica Villani

2015-01-01

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

Linear electro-optic coefficient in multilayer self-organized InAs quantum dot structures

NARCIS (Netherlands)

Akca, I.B.; Dana, A.; Aydinli, A.; Rossetti, M.; Li, L.; Dagli, N.; Fiore, A.

2007-01-01

The electro-optic coefficients of self-organized InAs quantum dot layers in molecular beam epitaxy grown laser structures in reverse bias have been investigated. Enhanced electrooptic coefficients compared to bulk GaAs were observed.

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

Science.gov (United States)

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

2015-01-01

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

Molecular structure impacts on secondary organic aerosol formation from glycol ethers

Science.gov (United States)

Li, Lijie; Cocker, David R.

2018-05-01

Glycol ethers, a class of widely used solvents in consumer products, are often considered exempt as volatile organic compounds based on their vapor pressure or boiling points by regulatory agencies. However, recent studies found that glycol ethers volatilize at ambient conditions nearly as rapidly as the traditional high-volatility solvents indicating the potential of glycol ethers to form secondary organic aerosol (SOA). This is the first work on SOA formation from glycol ethers. The impact of molecular structure, specifically -OH, on SOA formation from glycol ethers and related ethers are investigated in the work. Ethers with and without -OH, with methyl group hindrance on -OH and with -OH at different location are studied in the presence of NOX and under "NOX free" conditions. Photooxidation experiments under different oxidation conditions confirm that the processing of ethers is a combination of carbonyl formation, cyclization and fragmentation. Bulk SOA chemical composition analysis and oxidation products identified in both gas and particle phase suggests that the presence and location of -OH in the carbon bond of ethers determine the occurrence of cyclization mechanism during ether oxidation. The cyclization is proposed as a critical SOA formation mechanism to prevent the formation of volatile compounds from fragmentation during the oxidation of ethers. Glycol ethers with -CH2-O-CH2CH2OH structure is found to readily form cyclization products, especially with the presence of NOx, which is more relevant to urban atmospheric conditions than without NOx. Glycol ethers are evaluated as dominating SOA precursors among all ethers studied. It is estimated that the contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources. The contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources and will play a more important role in future anthropogenic SOA

The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

Energy Technology Data Exchange (ETDEWEB)

Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby (Michigan)

2014-10-02

{alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

Organic-inorganic semiconductor hybrid systems. Structure, morphology, and electronic properties

Energy Technology Data Exchange (ETDEWEB)

El Helou, Mira

2012-08-22

This dissertation addresses the preparation and characterization of hybrid semiconducting systems combining organic with inorganic materials. Characterization methods used included to determine the structure, morphology, and thermal stability comprised X-ray diffraction (XRD), atomic force microscopy (AFM), thermal desorption spectroscopy (TDS), and X-ray photoelectron spectroscopy (XPS). One organic-inorganic semiconducting system was pentacene (C{sub 22}H{sub 14}) and zinc oxide. This interface was investigated in detail for pentacene on an oxygen-terminated zinc oxide surface, i.e. ZnO(000 anti 1). An extended study on the promising p-n junction was carried out for pentacene on ZnO with different orientations which exhibit different chemical and structural characteristics: ZnO(000 anti 1), ZnO(0001), and ZnO(10 anti 10). Moreover, the organic crystal structure of pentacene was selectively tuned by carefully choosing the substrate temperature. This defined interface with a physisorbed pentacene layer on ZnO was characterized by optical absorption which depends on the temperature of the measured system, the pentacene film thickness, and the molecular orientation and packing. The high quality of the pentacene films allowed in one case to characterize the Davydov splitting by linear polarized light focused on a single crystallite. Another subject in the field of organic-inorganic hybrid materials comprised conjugated dithiols used as self-assembled monolayers (SAMs) for immobilizing semiconducting CdS nanoparticles (NPs) on Au substrates. It was demonstrated that an appropriate selection and preparation of the conjugated SAMs is crucial for building up a light-addressable potentiometric sensor with a sufficient efficiency. An optimized electron transfer was achieved with SAMs of long range ordering, high stability, and adequate conductivity. This was examined for different linkers and was best for stilbenedithiol immobilized in solution at higher temperatures. Due

Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures.

Science.gov (United States)

Saeidi, Nima; Karmelek, Kathryn P; Paten, Jeffrey A; Zareian, Ramin; DiMasi, Elaine; Ruberti, Jeffrey W

2012-10-01

Collagen in vertebrate animals is often arranged in alternating lamellae or in bundles of aligned fibrils which are designed to withstand in vivo mechanical loads. The formation of these organized structures is thought to result from a complex, large-area integration of individual cell motion and locally-controlled synthesis of fibrillar arrays via cell-surface fibripositors (direct matrix printing). The difficulty of reproducing such a process in vitro has prevented tissue engineers from constructing clinically useful load-bearing connective tissue directly from collagen. However, we and others have taken the view that long-range organizational information is potentially encoded into the structure of the collagen molecule itself, allowing the control of fibril organization to extend far from cell (or bounding) surfaces. We here demonstrate a simple, fast, cell-free method capable of producing highly-organized, anistropic collagen fibrillar lamellae de novo which persist over relatively long-distances (tens to hundreds of microns). Our approach to nanoscale organizational control takes advantage of the intrinsic physiochemical properties of collagen molecules by inducing collagen association through molecular crowding and geometric confinement. To mimic biological tissues which comprise planar, aligned collagen lamellae (e.g. cornea, lamellar bone or annulus fibrosus), type I collagen was confined to a thin, planar geometry, concentrated through molecular crowding and polymerized. The resulting fibrillar lamellae show a striking resemblance to native load-bearing lamellae in that the fibrils are small, generally aligned in the plane of the confining space and change direction en masse throughout the thickness of the construct. The process of organizational control is consistent with embryonic development where the bounded planar cell sheets produced by fibroblasts suggest a similar confinement/concentration strategy. Such a simple approach to nanoscale

The study of features of the structural organization of the au-tomated information processing system of the collective type

Science.gov (United States)

Nikolaev, V. N.; Titov, D. V.; Syryamkin, V. I.

2018-05-01

The comparative assessment of the level of channel capacity of different variants of the structural organization of the automated information processing systems is made. The information processing time assessment model depending on the type of standard elements and their structural organization is developed.

Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit.

Science.gov (United States)

Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

2016-01-08

One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ∼3  nm. Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.

The chemical structure of the insoluble organic matter from carbonaceous meteorites

Science.gov (United States)

Derenne, S.; Robert, F.

2008-09-01

Carbonaceous chondrites are the most primitive objects of the solar system. They contain substantial amounts of carbon (up to 3%), mostly occurring in macromolecular insoluble organic matter (IOM). This IOM is generally considered as a record of interstellar synthesis and may contain precursors of prebiotic molecules possibly deposited on earth by meteoritic bombardments. For these reasons, chondritic IOM has been raising interest for long and it is therefore of special interest to decipher its chemical structure. It is now well established that the chemical structure of this macromolecular material is based on aromatic moieties linked by short aliphatic chains and comprising substantial amounts of heteroatoms. However, its precise chemical structure could only be recently specified. The aim of this presentation is to propose a molecular model for the chemical structure of IOM isolated from non-metamorphosed carbonaceous chondrites. This model is derived from a large set of data obtained through a combination of techniques including various spectrocopies, high resolution transmission electron microscopy (HRTEM) and chemical and thermal degradations. Cosmochemical implications of such a structure will also be discussed.

Electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ

DEFF Research Database (Denmark)

Sing, M.; Schwingenschlögl, U.; Claessen, R.

2003-01-01

We study the electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ by means of density-functional band theory, Hubbard model calculations, and angle-resolved photoelectron spectroscopy (ARPES). The experimental spectra reveal significant quantitative and qualitative......-dimensional Hubbard model for the low-energy spectral behavior is attributed to interchain coupling and the additional effect of electron-phonon interaction....

Anthraquinone with tailored structure for a nonaqueous metal-organic redox flow battery.

Science.gov (United States)

Wang, Wei; Xu, Wu; Cosimbescu, Lelia; Choi, Daiwon; Li, Liyu; Yang, Zhenguo

2012-07-07

A nonaqueous, hybrid metal-organic redox flow battery based on tailored anthraquinone structure is demonstrated to have an energy efficiency of ~82% and a specific discharge energy density similar to those of aqueous redox flow batteries, which is due to the significantly improved solubility of anthraquinone in supporting electrolytes.

Multiscale pore structure and its effect on gas transport in organic-rich shale

Science.gov (United States)

Wu, Tianhao; Li, Xiang; Zhao, Junliang; Zhang, Dongxiao

2017-07-01

A systematic investigation of multiscale pore structure in organic-rich shale by means of the combination of various imaging techniques is presented, including the state-of-the-art Helium-Ion-Microscope (HIM). The study achieves insight into the major features at each scale and suggests the affordable techniques for specific objectives from the aspects of resolution, dimension, and cost. The pores, which appear to be isolated, are connected by smaller pores resolved by higher-resolution imaging. This observation provides valuable information, from the microscopic perspective of pore structure, for understanding how gas accumulates and transports from where it is generated. A comprehensive workflow is proposed based on the characteristics acquired from the multiscale pore structure analysis to simulate the gas transport process. The simulations are completed with three levels: the microscopic mechanisms should be taken into consideration at level I; the spatial distribution features of organic matter, inorganic matter, and macropores constitute the major issue at level II; and the microfracture orientation and topological structure are dominant factors at level III. The results of apparent permeability from simulations agree well with the values acquired from experiments. By means of the workflow, the impact of various gas transport mechanisms at different scales can be investigated more individually and precisely than conventional experiments.

CONVERSION PRODUCT STRUCTURE AS TOOL TO INCREASE YIELD PROCESSING ORGANIZATIONS

Directory of Open Access Journals (Sweden)

A. I. Khorev

2014-01-01

Full Text Available The authors' analysis of the performance of organizations, processing raw materials of agricultural origin, in particular, dealing with meat processing, identified the need to develop tools to increase their profitability. Unlike common approaches to assessing the profitability of the processing organizations, taking into account only the interests of the organization's leadership and buyers of products, the authors proposed and implemented a concept based on the interests of participants in the triune balance business activities: owners of capital, management organizations and consumers. As one of the tools for improving the yield of processing organizations are invited to transform their product mix of economic evaluations of profitability of each product line positions. Russian researchers income from product sales are traditionally measured by indicators such as net income, income from sales, profit margins and profitability level - in terms of return on sales. The disadvantage of using these indicators, according to the authors, is their lack of objectivity in the evaluation of the effectiveness of investment business owners. In this work was used unconventional and non-proliferation in the Russian practice, the rate of economic value added (EVA, a built - in system of profitability assortment positions. As indicators, the production of a particular product line units proposed and used two quantitative indicators - EVA level per unit of production and profitability of production (for EVA, as well as a quality parameter - the level of demand. Developed by the evaluation program transformation product structure represented as a matrix management capabilities, allowing to achieve a balance of interests of the triune main participants in business activity.

Organic Photovoltaic Structures as Photo-active Electrodes

International Nuclear Information System (INIS)

Gustafson, Matthew P.; Clark, Noel; Winther-Jensen, Bjorn; MacFarlane, Douglas R.

2014-01-01

This study demonstrated the novel use of a bulk heterojunction (BHJ), as present in modern organic solar cells, as a light-assisted electrocatalyst for water electrolysis reactions. Two separate organic photo-voltaic electrode structures were designed for targeting both the reduction, (ITO-PET/PEDOT:PSS/P3HT:PCBM)* and oxidation, (ITO-PET/ZnO/P3HT:PCBM)* reactions of water, denoted as OPE-R and OPE-O respectively. The OPE-R electrode supported both the proton reduction reaction (PRR) and oxygen reduction reaction (ORR) achieving photocurrents of -0.04 mAcm −2 (ORR) and -0.03 mAcm −2 (PRR) and a photovoltage of 0.50 V (ORR) and onset photovoltage at -0.59 V (PRR). By comparison, the OPE-O electrode achieved photocurrents of 0.15 mAcm −2 and photovoltages of 0.35 V for the water oxidation reaction (WOR). Both BHJ designs confirmed evidence of photo-enhanced Bulk Heterojunction Electrode (BHE) activity. The stability and sources of electrode degradation were also studied, with the OPE-O electrode proving to be more stable than the OPE-R electrode, most likely due to the PEDOT:PSS layer and PSS migration in the presence of water. *Indium Tin Oxide (ITO), Polyethylene Terephthalate (PET), Poly(3,4-ethylenedioxythiophene) (PEDOT), Polystyrenesulfonate acid (PSS), Poly(3-hexylthiophene) (P3HT), Phenyl-C 61 -Butyric acid Methyl ester (PCBM), Zinc Oxide (ZnO)

Evolution and structural organization of the C proteins of paramyxovirinae.

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Michael K Lo

Full Text Available The phosphoprotein (P gene of most Paramyxovirinae encodes several proteins in overlapping frames: P and V, which share a common N-terminus (PNT, and C, which overlaps PNT. Overlapping genes are of particular interest because they encode proteins originated de novo, some of which have unknown structural folds, challenging the notion that nature utilizes only a limited, well-mapped area of fold space. The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar organization: a variable, disordered N-terminus and a conserved, α-helical C-terminus. We confirmed this predicted organization by biophysically characterizing recombinant C proteins from Tupaia paramyxovirus (measles group and human parainfluenza virus 1 (Sendai group. We also found that the C of the measles and Nipah groups have statistically significant sequence similarity, indicating a common origin. Although the C of the Sendai group lack sequence similarity with them, we speculate that they also have a common origin, given their similar genomic location and structural organization. Since C is dispensable for viral replication, unlike PNT, we hypothesize that C may have originated de novo by overprinting PNT in the ancestor of Paramyxovirinae. Intriguingly, in measles virus and Nipah virus, PNT encodes STAT1-binding sites that overlap different regions of the C-terminus of C, indicating they have probably originated independently. This arrangement, in which the same genetic region encodes simultaneously a crucial functional motif (a STAT1-binding site and a highly constrained region (the C-terminus of C, seems paradoxical, since it should severely reduce the ability of the virus to adapt. The fact that it originated twice suggests that it must be balanced by an evolutionary advantage, perhaps from reducing the size of the genetic region vulnerable to mutations.

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing.

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Subha, Bakthavachallam; Song, Young Chae; Woo, Jung Hui

2015-09-15

The present study aims to optimize the slow release biostimulant ball (BSB) for bioremediation of contaminated coastal sediment using response surface methodology (RSM). Different bacterial communities were evaluated using a pyrosequencing-based approach in contaminated coastal sediments. The effects of BSB size (1-5cm), distance (1-10cm) and time (1-4months) on changes in chemical oxygen demand (COD) and volatile solid (VS) reduction were determined. Maximum reductions of COD and VS, 89.7% and 78.8%, respectively, were observed at a 3cm ball size, 5.5cm distance and 4months; these values are the optimum conditions for effective treatment of contaminated coastal sediment. Most of the variance in COD and VS (0.9291 and 0.9369, respectively) was explained in our chosen models. BSB is a promising method for COD and VS reduction and enhancement of SRB diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India

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Pravin Dudhagara

2015-06-01

Full Text Available Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP. Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%, Fibrobacter intestinalis (12% and Candidatus Cloacamonas acidaminovorans (11%. Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%, Methanoculleus chikugoensis (12% and Methanolinea tarda (11% were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.

Seeking structure in social organization: compensatory control and the psychological advantages of hierarchy.

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Friesen, Justin P; Kay, Aaron C; Eibach, Richard P; Galinsky, Adam D

2014-04-01

Hierarchies are a ubiquitous form of human social organization. We hypothesized that 1 reason for the prevalence of hierarchies is that they offer structure and therefore satisfy the core motivational needs for order and control relative to less structured forms of social organization. This hypothesis is rooted in compensatory control theory, which posits that (a) individuals have a basic need to perceive the world as orderly and structured, and (b) personal and external sources of control are capable of satisfying this need because both serve the comforting belief that the world operates in an orderly fashion. Our first 2 studies confirmed that hierarchies were perceived as more structured and orderly relative to egalitarian arrangements (Study 1) and that working in a hierarchical workplace promotes a feeling of self-efficacy (Study 2). We threatened participants' sense of personal control and measured perceptions of and preferences for hierarchy in 5 subsequent experiments. Participants who lacked control perceived more hierarchy occurring in ambiguous social situations (Study 3) and preferred hierarchy more strongly in workplace contexts (Studies 4-5). We also provide evidence that hierarchies are indeed appealing because of their structure: Preference for hierarchy was higher among individuals high in Personal Need for Structure and a control threat increased preference for hierarchy even among participants low in Personal Need for Structure (Study 5). Framing a hierarchy as unstructured reversed the effect of control threat on hierarchy (Study 6). Finally, hierarchy-enhancing jobs were more appealing after control threat, even when they were low in power and status (Study 7). (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Recent progress in predicting structural and electronic properties of organic solids with the van der Waals density functional

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Yanagisawa, Susumu, E-mail: shou@sci.u-ryukyu.ac.jp [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213 (Japan); Okuma, Koji; Inaoka, Takeshi [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213 (Japan); Hamada, Ikutaro, E-mail: Hamada.Ikutaro@nims.go.jp [International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba 305-0044 (Japan)

2015-10-01

Highlights: • Review of theoretical studies on organic solids with the density-functional methods. • van der Waals (vdW)-inclusive methods to predict cohesive properties of oligoacenes. • A variant of the vdW density functional describes the structures accurately. • The molecular configuration and conformation crucially affects the band dispersion. - Abstract: We review recent studies on electronic properties of the organic solids with the first-principles electronic structure methods, with the emphasis on the roles of the intermolecular van der Waals (vdW) interaction in electronic properties of the organic semiconductors. After a brief summary of the recent vdW inclusive first-principle theoretical methods, we discuss their performance in predicting cohesive properties of oligoacene crystals as examples of organic crystals. We show that a variant of the van der Waals density functional describes structure and energetics of organic crystals accurately. In addition, we review our recent study on the zinc phthalocyanine crystal and discuss the importance of the intermolecular distance and orientational angle in the band dispersion. Finally, we draw some general conclusions and the future perspectives.