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Sample records for pyrosequencing structural organization

  1. Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing.

    Science.gov (United States)

    Schoebel, C N; Brodbeck, S; Buehler, D; Cornejo, C; Gajurel, J; Hartikainen, H; Keller, D; Leys, M; Ríčanová, S; Segelbacher, G; Werth, S; Csencsics, D

    2013-03-01

    Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab-tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time-consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.

  2. Microbial community structure of Arctic seawater as revealed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    LI Yang; WANG Zhen; LIN Xuezheng

    2016-01-01

    This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95%and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.

  3. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Institute of Scientific and Technical Information of China (English)

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

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

    Science.gov (United States)

    Song, Qinxin; Wei, Guijiang; Zhou, Guohua

    2014-07-01

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

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

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    Sébastien Monchy

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

  6. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

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    Ru Li

    Full Text Available It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

  7. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

    Science.gov (United States)

    Li, Ru; Khafipour, Ehsan; Krause, Denis O; Entz, Martin H; de Kievit, Teresa R; Fernando, W G Dilantha

    2012-01-01

    It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional) and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat) was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

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

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    Neng Fei eWang

    2015-10-01

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

  9. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    OpenAIRE

    Lee, Charles K.; Craig W. Herbold; Polson, Shawn W.; K Eric Wommack; Williamson, Shannon J.; McDonald, Ian R.; S. Craig Cary

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure est...

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

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    Ailin Wang

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

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

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

    2017-04-01

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

  12. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Charles K Lee

    Full Text Available Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  13. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Science.gov (United States)

    Lee, Charles K; Herbold, Craig W; Polson, Shawn W; Wommack, K Eric; Williamson, Shannon J; McDonald, Ian R; Cary, S Craig

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  14. Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms

    Science.gov (United States)

    Organic farming is a growing field of agriculture that is benign on the environment but there are contradictory reports about the impact of these practices on the soil microbial community, i.e. some studies showed higher microbial diversity in organic farms but others showed no differences in divers...

  15. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    DEFF Research Database (Denmark)

    Møller, Annette K.; Søborg, Ditte A.; Abu Al-Soud, Waleed;

    2013-01-01

    The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition...

  16. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    DEFF Research Database (Denmark)

    Møller, Annette; Søborg, Ditte Andreasen; Al-Soud, Waleed Abu

    2013-01-01

    The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition...

  17. 454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils.

    Science.gov (United States)

    Makonde, Huxley M; Mwirichia, Romano; Osiemo, Zipporah; Boga, Hamadi I; Klenk, Hans-Peter

    2015-01-01

    Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites' gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40-58 %), Spirochaetes (10-70 %), Firmicutes (17-27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28-45 %), Actinobacteria (20-40 %) and Proteobacteria (18-24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to

  18. Pyrosequencing-based assessment of soil bacterial communities within soil aggregates: Linking structure to C storage

    Science.gov (United States)

    Alterations in soil structural properties created by agricultural management practices have a significant influence on soil aggregation, which manages the chemical and physical heterogeneity of soil properties, and, consequently, the distribution of microorganisms and their activity among aggregates...

  19. 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.

  20. Pyrosequencing and mid-infrared spectroscopy techniques reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

    Science.gov (United States)

    This study integrated physical, chemical, and molecular techniques to assess relationships between soil bacterial community structures and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this g...

  1. Phylogeny of intestinal ciliates, including Charonina ventriculi, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis.

    Science.gov (United States)

    Kittelmann, Sandra; Devente, Savannah R; Kirk, Michelle R; Seedorf, Henning; Dehority, Burk A; Janssen, Peter H

    2015-04-01

    The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates, Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence in situ hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence, Charonina ventriculi was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

  2. Aggregate stratification assessment of soil bacterial communities and organic matter composition: Coupling pyrosequencing and mid-infrared spectroscopy techniques

    Science.gov (United States)

    This study integrated physical, chemical, and molecular techniques to assess relationships between soil bacterial communities and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this goal soil ...

  3. 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)

    Shen, Zongzhuan; Wang, Dongsheng; 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.

  4. Deep 16S rRNA pyrosequencing reveals a bacterial community associated with Banana Fusarium Wilt disease suppression induced by bio-organic fertilizer application.

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    Zongzhuan Shen

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  6. Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA.

    Science.gov (United States)

    Wu, Shijin; Li, Yuan; Wang, Penghua; Zhong, Li; Qiu, Lequan; Chen, Jianmeng

    2016-04-01

    The environmental risk of fluoride and chloride pollution is pronounced in soils adjacent to solar photovoltaic sites. The elevated levels of fluoride and chloride in these soils have had significant impacts on the population size and overall biological activity of the soil microbial communities. The microbial community also plays an essential role in remediation of these soils. Questions remain as to how the fluoride and chloride contamination and subsequent remediation at these sites have impacted the population structure of the soil microbial communities. We analyzed the microbial communities in soils collected from close to a solar photovoltaic enterprise by pyrosequencing of the 16S rRNA tag. In addition, we used multivariate statistics to identity the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa and sharing significant correlations with different degrees of fluoride and chloride contamination. The contaminated soils harbored abundant bacteria that were probably resistant to the high acidity, high fluoride and chloride concentration, and high osmotic pressure environment. The dominant genera were Sphingomonas, Subgroup_6_norank, Clostridium sensu stricto, Nitrospira, Rhizomicrobium, and Acidithiobacillus. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.

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

    NARCIS (Netherlands)

    Claesson, M.J.; O'Sullivan, O.; Wang, Q.; Nikkilä, J.; Marchesi, J.R.; Smidt, H.; Vos, de W.M.; Ross, R.P.; O'Toole, P.W.

    2009-01-01

    BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods

  8. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Daniel H. [Cornell Univ., Ithaca, NY (United States)

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  9. Structural aspects of agent organizations

    NARCIS (Netherlands)

    D. Grossi; F. Dignum

    2009-01-01

    In this chapter we investigate how organizations can be represented as graphs endowed with formal semantics. We distinguish different dimensions of organizations. Each of these dimensions leads to a different structure in the organizational graph. By giving the graphs a formal semantics in Descripti

  10. 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.

  11. 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.

  12. Gender Structure and Spatial Organization

    Directory of Open Access Journals (Sweden)

    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.

  13. 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

  14. 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...

  15. Automatizations processes influence on organizations structure

    Directory of Open Access Journals (Sweden)

    Vace¾ Rastislav

    2003-09-01

    Full Text Available Has been influenced organization structure on processes? If yes, what is the rate? Is approach toward organization structures bordered by aspect of hierarchy? On these and same questions replay that contribution which in detail sight describe uncertainty managing of process in dependence on the type of organization structure.

  16. Removing Noise From Pyrosequenced Amplicons

    Directory of Open Access Journals (Sweden)

    Davenport Russell J

    2011-01-01

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

  17. Polymer Structure--Organic Aspects (Definitions).

    Science.gov (United States)

    Carraher, Charles E., Jr.; Seymour, Raymond B.

    1988-01-01

    Lists alphabetically the definitions of key organic-based terms used in characterizing the structure of polymers. Includes several common polymers, some of their uses and their respective structures. (CW)

  18. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.

    Science.gov (United States)

    Tedersoo, Leho; Nilsson, R Henrik; Abarenkov, Kessy; Jairus, Teele; Sadam, Ave; Saar, Irja; Bahram, Mohammad; Bechem, Eneke; Chuyong, George; Kõljalg, Urmas

    2010-10-01

    • Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood. • This study compares the performance of pyrosequencing and traditional sequencing for species' recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses. • Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing. • Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz.

  19. Shifts in Bacterial Community Structure in the Process of Composting of Organic Wastes

    Directory of Open Access Journals (Sweden)

    Polina Galitskaya

    2016-04-01

    Full Text Available Using 454 pyrosequencing, changes in the community structure of composting bacteria were estimated over 270 days. The compost contained the organic fraction of municipal solid waste, sawdust polluted by oil, and sewage sludge. All of these wastes are typical for a Russian city and they were obtained in Kazan (Tatarstan Republic, Russia. In the initial stage of composting, the taxa Lactobacialles, Rhodospiralles, Burkholderiales, and Xanthmonadales dominated in the compost. By the end of the thermophilic stage, the dominant species changed: typical compost inhabitants belonging to the taxa Flavobacteriales, Chitinophagaceae, and Bacterioidetes, as well as non-typical taxa Ectothiorhodospiraceae and Parvibaculum sp., were observed in the compost. The presence of the latter two taxa may be explained by the presence of oil-polluted sawdust in the composting mixture. In the later stage, the dominant taxa remained the same; however, their relative abundance declined.

  20. 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.

  1. Psychodiagnosis of personality structure: psychotic personality organization.

    Science.gov (United States)

    Acklin, M W

    1992-06-01

    Recent developments in Rorschach psychology, including nomothetic approaches focused on scores, ratios, and indices and idiographic approaches focused on content emerging from psychoanalytic theory, offer the Rorschach clinician a rich and potent interpretive methodology. This article examines the structural diagnosis of personality organization with a focus on psychotic personality structure. Rorschach approaches to the differential diagnosis of psychotic personality organization are presented. The Rorschach is viewed as indispensible in the differential diagnosis of personality organization, especially in the so-called "borderline" cases.

  2. Pyrosequencing for microbial identification and characterization.

    Science.gov (United States)

    Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

    2013-08-22

    Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

  3. Identification of bacteria directly from positive blood culture samples by DNA pyrosequencing of the 16S rRNA gene.

    Science.gov (United States)

    Motoshima, Maiko; Yanagihara, Katsunori; Morinaga, Yoshitomo; Matsuda, Junichi; Hasegawa, Hiroo; Kohno, Shigeru; Kamihira, Shimeru

    2012-11-01

    Rapid identification of the causative bacteria of sepsis in patients can contribute to the selection of appropriate antibiotics and improvement of patients' prognosis. Genotypic identification is an emerging technology that may provide an alternative method to, or complement, established phenotypic identification procedures. We evaluated a rapid protocol for bacterial identification based on PCR and pyrosequencing of the V1 and V3 regions of the 16S rRNA gene using DNA extracted directly from positive blood culture samples. One hundred and two positive blood culture bottles from 68 patients were randomly selected and the bacteria were identified by phenotyping and pyrosequencing. The results of pyrosequencing identification displayed 84.3 and 64.7 % concordance with the results of phenotypic identification at the genus and species levels, respectively. In the monomicrobial samples, the concordance between the results of pyrosequencing and phenotypic identification at the genus level was 87.0 %. Pyrosequencing identified one isolate in 60 % of polymicrobial samples, which were confirmed by culture analysis. Of the samples identified by pyrosequencing, 55.7 % showed consistent results in V1 and V3 targeted sequencing; other samples were identified based on the results of V1 (12.5 %) or V3 (31.8 %) sequencing alone. One isolate was erroneously identified by pyrosequencing due to high sequence similarity with another isolate. Pyrosequencing identified one isolate that was not detected by phenotypic identification. The process of pyrosequencing identification can be completed within ~4 h. The information provided by DNA-pyrosequencing for the identification of micro-organisms in positive blood culture bottles is accurate and could prove to be a rapid and useful tool in standard laboratory practice.

  4. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.

    Science.gov (United States)

    Kirchman, David L; Cottrell, Matthew T; Lovejoy, Connie

    2010-05-01

    Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the 'seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones.

  5. A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis.

    Science.gov (United States)

    Zhang, Xiaojun; Yue, Siqing; Zhong, Huihui; Hua, Weiying; Chen, Ruijia; Cao, Youfang; Zhao, Liping

    2011-07-01

    There is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. In this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. By both technologies, 16S rRNA gene analysis indicated that the bacteria in the sample were closely related to, for example, Proteobacteria, Actinobacteria, and Bacteroidetes. The sequences belonging to Rhodococcus were the most predominant, and Pseudomonas, Sphingomonas, Acidovorax, and Zoogloea were also abundant. Both methods revealed a similar overall bacterial community structure. However, the 622 pyrosequencing reads of the hypervariable V3 region of the 16S rRNA gene revealed much higher bacterial diversity than the 130 sequences from the full-length 16S rRNA gene clone library. The 92 operational taxonomic unit (OTUs) detected using pyrosequencing belonged to 45 families, whereas the 37 OTUs found in the clone library belonged to 25 families. Most sequences obtained from the clone library had equivalents in the pyrosequencing reads. However, 64 OTUs detected by pyrosequencing were not represented in the clone library. Our results demonstrate that pyrosequencing of the V3 region of the 16S rRNA gene is not only a powerful tool for discovering low-abundance bacterial populations but is also reliable for dissecting the bacterial community structure in a wastewater environment.

  6. Structural Dynamics Within and Between Organizations.

    Science.gov (United States)

    Fombrun, Charles J.

    1986-01-01

    The concept of structure is recast as an instantaneous correspondence between an infrastructure, a sociostructure, and a superstructure--manifestations of collective life juxtaposed through technological solutions, political exchanges, and social interpretations involving organizations. Ultimately, structuring is a dialectical unfolding of…

  7. [Application of pyrosequencing in detection of common pathogens in sepsis].

    Science.gov (United States)

    Hu, Ziyou; Han, Hui; Zeng, Yong; Wu, Bingyi

    2013-07-01

    To apply pyrosequencing technique in the detection of the common pathogens in sepsis. The primers for amplification and sequencing in pyrosequencing were designed according to alignment of the bacterial 16S rRNA sequence. Bacterial genomic DNA was extracted for pyrosequencing, and the pathogen species were determined according to the sequencing data obtained. Pyrosequencing effectively yielded the sequencing data of the 28 bp sequences of the pathogens and clearly distinguished the pathogen species of Streptococcus pyogenes, Streptococcus pneumonia, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Neisseria meningitides, and Salmonella, but failed to distinguish Staphylococcus epidermidis from Staphylococcus aureus. Pyrosequencing technique can effectively distinguish the common pathogens in sepsis at the species level.

  8. Predicting crystal structures of organic compounds.

    Science.gov (United States)

    Price, Sarah L

    2014-04-07

    Currently, organic crystal structure prediction (CSP) methods are based on searching for the most thermodynamically stable crystal structure, making various approximations in evaluating the crystal energy. The most stable (global minimum) structure provides a prediction of an experimental crystal structure. However, depending on the specific molecule, there may be other structures which are very close in energy. In this case, the other structures on the crystal energy landscape may be polymorphs, components of static or dynamic disorder in observed structures, or there may be no route to nucleating and growing these structures. A major reason for performing CSP studies is as a complement to solid form screening to see which alternative packings to the known polymorphs are thermodynamically feasible.

  9. Getting from Organ- to Part- Structure

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Mortensen, Niels Henrik

    1997-01-01

    The paper gives definitions of organ and part and elaborate on the relations between organ, parts and production methods. The importance of the law of superimposed structures on part design is illustrated and a domain- and view concept is developed.The paper is a collective of overhead-copies, pu......The paper gives definitions of organ and part and elaborate on the relations between organ, parts and production methods. The importance of the law of superimposed structures on part design is illustrated and a domain- and view concept is developed.The paper is a collective of overhead......-copies, published in an informed binder from the 13th WDK' Workshop at Rigi....

  10. Minerals with metal-organic framework structures

    Science.gov (United States)

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

    2016-01-01

    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. PMID:27532051

  11. Pyrosequencing Analysis for Breast Cancer DNA Methylome.

    Science.gov (United States)

    Kuscu, Cem; Kuscu, Canan

    2016-01-01

    Unraveling DNA methylation profile of tumor is important for the diagnosis and treatment of cancer patients. Because of the heterogeneity of clinical samples, it is very difficult to get methylation profile of only tumor cells. Laser capture Microdissection (LCM) is giving us a chance to isolate the DNA only from the tumor cells without any stroma cell's DNA contamination. Once we capture the breast tumor cells, we can isolate the genomic DNA which is followed by the bisulfite treatment in which unmethylated cytosines of the CG pairs are converted into uracil; however, methylated cytosine does not go into any chemical change during this reaction. Next, bisulfite treated DNA is used in the regular PCR reaction to get a single band PCR amplicon which will be used as a template for the pyrosequencing. Pyrosequencing is a powerful method to make a quantitative methylation analysis for each specific CG pair.

  12. Pyrosequencing assay for rapid identification of Mycobacterium tuberculosis complex species

    Directory of Open Access Journals (Sweden)

    Boukadida Jalel

    2011-10-01

    Full Text Available Abstract Background Identification of the Mycobacterium tuberculosis complex organisms to the species level is important for diagnostic, therapeutic and epidemiologic perspectives. Indeed, isolates are routinely identified as belonging to the M. tuberculosis complex without further discrimination in agreement with the high genomic similarity of the M. tuberculosis complex members and the resulting complex available identification tools. Findings We herein develop a pyrosequencing assay analyzing polymorphisms within glpK, pykA and gyrB genes to identify members of the M. tuberculosis complex at the species level. The assay was evaluated with 22 M. tuberculosis, 21 M. bovis, 3 M. caprae, 3 M. microti, 2 M. bovis BCG, 2 M. pinnipedii, 1 M. canettii and 1 M. africanum type I isolates. The resulted pyrograms were consistent with conventional DNA sequencing data and successfully identified all isolates. Additionally, 127 clinical M. tuberculosis complex isolates were analyzed and were unambiguously identified as M. tuberculosis. Conclusion We proposed a pyrosequencing-based scheme for the rapid identification of M. tuberculosis complex isolates at the species level. The assay is robust, specific, rapid and can be easily introduced in the routine activity.

  13. Growth of pseudomorphic structures through organic epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Kaviyil, Sreejith Embekkat; Sassella, Adele; Borghesi, Alessandro [Department of Materials Science, Universita degli Studi di Milano Bicocca, Via R. Cozzi 53, I-20125 Milan (Italy); Campione, Marcello [Department of Earth and Environmental Sciences, Universita degli Studi di Milano Bicocca, Piazza della Scienza 4, I-20126 Milan (Italy); Su Genbo; He Youping [Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou 350002 (China); Chen Chenjia [Department of Physics, Peking University, Beijing 100871 (China)

    2012-12-14

    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 {alpha}-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.

  14. Band structure engineering in organic semiconductors

    Science.gov (United States)

    Schwarze, Martin; Tress, Wolfgang; Beyer, Beatrice; Gao, Feng; Scholz, Reinhard; Poelking, Carl; Ortstein, Katrin; Günther, Alrun A.; Kasemann, Daniel; Andrienko, Denis; Leo, Karl

    2016-06-01

    A key breakthrough in modern electronics was the introduction of band structure engineering, the design of almost arbitrary electronic potential structures by alloying different semiconductors to continuously tune the band gap and band-edge energies. Implementation of this approach in organic semiconductors has been hindered by strong localization of the electronic states in these materials. We show that the influence of so far largely ignored long-range Coulomb interactions provides a workaround. Photoelectron spectroscopy confirms that the ionization energies of crystalline organic semiconductors can be continuously tuned over a wide range by blending them with their halogenated derivatives. Correspondingly, the photovoltaic gap and open-circuit voltage of organic solar cells can be continuously tuned by the blending ratio of these donors.

  15. Pyrosequencing-An Alternative to Traditional Sanger Sequencing

    OpenAIRE

    2012-01-01

    Problem statement: Pyrosequencing has the potential to rapidly and reliably sequence DNA taking advantages over traditional Sanger di-deoxy sequencing approach. Approach: A comprehensive review of the literature on the principles, applications, challenges and prospects of pyrosequencing was performed. Results: Pyrosequencing was a DNA sequencing technology based on the sequencing-by-synthesis principle. It employs a series of four enzymes to accurately detect nucleic acid sequences during the...

  16. Advanced Structural Characterization of Organic Thin Films

    DEFF Research Database (Denmark)

    Gu, Yun

    In this thesis, the structural characterizations of three organic film systems are described. Several X-ray based techniques have been utilized for the characterizations for different research goals. The structures of N,N',N-trioctyltriazatriangulenium (Oct3-TATA+) salts have been investigated...... of small molecule and polymer layers is indicated by Flory- Huggins theory for the triisopropylsilylethynl pentacene (TIPS-PEN) and polystyrene blend films. In order to investigate the phase separated layers in the ink-jet printed films, we propose a method to measure diraction Bragg peaks by X...

  17. Advanced Structural Characterization of Organic Thin Films

    DEFF Research Database (Denmark)

    Gu, Yun

    In this thesis, the structural characterizations of three organic film systems are described. Several X-ray based techniques have been utilized for the characterizations for different research goals. The structures of N,N',N-trioctyltriazatriangulenium (Oct3-TATA+) salts have been investigated...... of small molecule and polymer layers is indicated by Flory- Huggins theory for the triisopropylsilylethynl pentacene (TIPS-PEN) and polystyrene blend films. In order to investigate the phase separated layers in the ink-jet printed films, we propose a method to measure diraction Bragg peaks by X...

  18. 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.

  19. Wolbachia Sequence Typing in Butterflies Using Pyrosequencing.

    Science.gov (United States)

    Choi, Sungmi; Shin, Su-Kyoung; Jeong, Gilsang; Yi, Hana

    2015-09-01

    Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.

  20. Organic light emitting diodes with structured electrodes

    Science.gov (United States)

    Mao, Samuel S.; Liu, Gao; Johnson, Stephen G.

    2012-12-04

    A cathode that contain nanostructures that extend into the organic layer of an OLED has been described. The cathode can have an array of nanotubes or a layer of nanoclusters extending out from its surface. In another arrangement, the cathode is patterned and etched to form protruding nanostructures using a standard lithographic process. Various methods for fabricating these structures are provided, all of which are compatible with large-scale manufacturing. OLEDs made with these novel electrodes have greatly enhanced electron injection, have good environmental stability.

  1. Pyrosequencing-An Alternative to Traditional Sanger Sequencing

    Directory of Open Access Journals (Sweden)

    Fakruddin

    2012-01-01

    Full Text Available Problem statement: Pyrosequencing has the potential to rapidly and reliably sequence DNA taking advantages over traditional Sanger di-deoxy sequencing approach. Approach: A comprehensive review of the literature on the principles, applications, challenges and prospects of pyrosequencing was performed. Results: Pyrosequencing was a DNA sequencing technology based on the sequencing-by-synthesis principle. It employs a series of four enzymes to accurately detect nucleic acid sequences during the synthesis. Pyrosequencing had the potential advantages of accuracy, flexibility, parallel processing and could be easily automated. The technique dispenses with the need for labeled primers, labeled nucleotides and gel-electrophoresis. Pyrosequencing had opened up new possibilities for performing sequence-based DNA analysis. The method had been proven highly suitable for single nucleotide polymorphism analysis and sequencing of short stretches of DNA. Pyrosequencing had been successful for both confirmatory sequencing and de novo sequencing. By increasing the read length to higher scores and by shortening the sequence reaction time per base calling, pyrosequencing may take over many broad areas of DNA sequencing applications as the trend was directed to analysis of fewer amounts of specimens and large-scale settings, with higher throughput and lower cost. Conclusion/Recommendations: The Competitiveness of pyrosequencing with other sequencing methods can be improved in future."

  2. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  3. Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

    OpenAIRE

    2012-01-01

    “Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  4. Genotyping of FCN and MBL2 Polymorphisms Using Pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans Ole; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...

  5. Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess.

    Science.gov (United States)

    Sibley, C D; Church, D L; Surette, M G; Dowd, S E; Parkins, M D

    2012-10-01

    The polymicrobial nature of invasive pyogenic infections may be underestimated by routine culture practices, due to the fastidious nature of many organisms and the loss of viability during transport or from prior antibacterials. Pyrosequencing was performed on brain and liver abscesses and pleural fluid and compared to routine culture data. Forty-seven invasive pyogenic infection samples from 44 patients [6 intracerebral abscess (ICA), 21 pyogenic liver abscess (PLA), and 18 pleural fluid (PF) samples] were assayed. Pyrosequencing identified an etiologic microorganism in 100 % of samples versus 45 % by culture, p <0.01. Pyrosequencing was also more likely than traditional cultures to classify infections as polymicrobial, 91 % versus 17 %, p <0.001. The median number of genera identified by pyrosequencing compared to culture was 1 [interquartile range (IQR) 1-3] versus 0 (IQR 0-1) for ICA, 7 (IQR 1-15) versus 1 (IQR 0-1) for PLA, and 15 (IQR 9-19) versus 0 (IQR 0-1) for PF. Where organisms were cultured, they typically represented the numerically dominant species identified by pyrosequencing. Complex microbial communities are involved in invasive pyogenic infection of the lung, liver, and brain. Defining the polymicrobial nature of invasive pyogenic infections is the first step towards appreciating the clinical and diagnostic implications of these complex communities.

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Integral Design workshops: organization, structure and testing

    Directory of Open Access Journals (Sweden)

    Wim Zeiler

    2010-08-01

    Full Text Available 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 of the participants. The project was done in close cooperation with the professional societies with in the Dutch building design field. More than one hundred experienced professionals participated in the workshops. The workshops have become part of the permanent professional training program Dutch architectural society.

  8. Pyrosequencing for EGFR mutation detection: diagnostic accuracy and clinical implications.

    Science.gov (United States)

    Sahnane, Nora; Gueli, Rossana; Tibiletti, Maria G; Bernasconi, Barbara; Stefanoli, Michele; Franzi, Francesca; Pinotti, Graziella; Capella, Carlo; Furlan, Daniela

    2013-12-01

    EGFR-activating mutations predict responsiveness to EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) patients. Mutation screening is crucial to support therapeutic decisions and is commonly conducted using dideoxy sequencing, although its sensitivity is suboptimal in clinical settings. To evaluate the diagnostic performance of pyrosequencing and dideoxy sequencing, we examined EGFR mutation status in a retrospective cohort of 53 patients with NSCLCs clinically selected for TKI therapy and whose clinical outcome was available. Moreover, pyrosequencing quantitative results were compared with EGFR amplification data. EGFR mutations were investigated by pyrosequencing and by dideoxy sequencing. Detection rates of both methods were determined by titration assays using NCI-H1975 and HCC-827 cell lines. Increased EGFR copy number was assessed by fluorescence in situ hybridization (FISH). Pyrosequencing showed a higher detection rate than dideoxy sequencing. Tumor control rate of cases with mutant and wild-type EGFR was 86% and 29%, respectively. EGFR amplification was significantly associated with EGFR mutation and a positive correlation between high percentages of mutant alleles and clinical response to TKI was observed. We concluded that pyrosequencing is more sensitive than dideoxy sequencing in mutation screening for EGFR mutations. Detection rate of dideoxy sequencing was suboptimal when low frequencies of mutant alleles or low tumor cell contents were observed. Pyrosequencing enables quantification of mutant alleles that correlates well with increased EGFR copy number assessed by FISH. Pyrosequencing should be used in molecular diagnostic of NSCLC to appropriately select patients who are likely to benefit from TKI therapy.

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

    Directory of Open Access Journals (Sweden)

    Wu Xiong

    Full Text Available 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  11. Molecular identification of Paragonimus species by DNA pyrosequencing technology.

    Science.gov (United States)

    Tantrawatpan, Chairat; Intapan, Pewpan M; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Srichantaratsamee, Chutatip; Anamnart, Witthaya; Maleewong, Wanchai

    2013-06-01

    DNA pyrosequencing for PCR amplicons is an attractive strategy for the identification of microorganisms because of its short time performance for large number of samples. In this study, the primers targeting the fragment of ITS2 region of nuclear ribosomal RNA gene were newly developed for pyrosequencing-based identification of 6 Paragonimus species, Paragonimus bangkokensis, Paragonimus harinasutai, Paragonimus heterotremus, Paragonimus macrorchis, Paragonimus siamensis and Paragonimus westermani. Pyrosequencing determination of 39 nucleotides of partial ITS2 region could discriminate 6 Paragonimus species, and could also detect intra-species genetic variation of P. macrorchis. This DNA pyrosequencing-based identification can be a valuable tool to improve species-level identification of Paragonimus in the endemic areas.

  12. Matrix Organizational Structure and Its Effects Upon Education Organizations.

    Science.gov (United States)

    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…

  13. Structural studies of ultrathin organic films

    Science.gov (United States)

    Yim, Hyun

    1998-11-01

    Ultrathin organic films have been a focus of research due to the growing interest in optoelectronics and molecular electronics. In both areas, it is believed that self-assembled (SA) films and Langmuir-Blodgett (LB) films may provide the desired control of order at the molecular level. The tethering of polyglutamate molecules to surfaces is of special interest due to nonlinear optical properties which can be achieved when the molecules are oriented. The tethering of poly(benzyl-L-glutamate) to silicon has been done by polymerization of benzyl-L-glutamate-N-carboxyanhydride using self-assembled monolayers with various concentrations of amino end groups as initiating layers. X-ray reflectivity results show that a minimum concentration of initiator sites on the surface is required. The second tethering system is a polystyrene brush. The polystyrene brush is expected to give strong sensitivity to solvent swelling. The structure of the polystyrene brush, which was chemically grafted to a substrate, in poor solvent and its change at different temperatures were investigated by neutron reflectometry. When temperature increases up to 30sp°C, both the thickness and roughness increase greatly, which indicates that the polystyrene brush changes from a collapsed state to a theta state. Hairy-rod polyimide molecules are of interest due to their interesting physical properties. Multilayer films of preformed polyimide molecules (6FDA-C18) have been obtained for the first time by the LB technique. The multilayer films do not display a distinctively periodic structure. Upon annealing for a few hours at 180sp°C, the structure relaxes slightly. The alkyl side chain substituted polyimides (BACBF/BPDA) can form metastable monolayers for which the pressure-area isotherms vary markedly with side chain length. For the polyimide with octadecyl side chains, a sharp reduction in zero pressure area occurs between 20 and 24sp°C, suggesting an important change in side chain mobility

  14. Accurate taxonomic assignment of short pyrosequencing reads.

    Science.gov (United States)

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel

    2010-01-01

    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  15. Organic superconductors with an incommensurate anion structure

    Directory of Open Access Journals (Sweden)

    Tadashi Kawamoto and Kazuo Takimiya

    2009-01-01

    Full Text Available Superconducting incommensurate organic composite crystals based on the methylenedithio-tetraselenafulvalene (MDT-TSF series donors, where the energy band filling deviates from the usual 3/4-filled, are reviewed. The incommensurate anion potential reconstructs the Fermi surface for both (MDT-TSF(AuI20.436 and (MDT-ST(I30.417 neither by the fundamental anion periodicity q nor by 2q, but by 3q, where MDT-ST is 5H-2-(1,3-dithiol-2-ylidene-1,3-diselena-4,6-dithiapentalene, and q is the reciprocal lattice vector of the anion lattice. The selection rule of the reconstructing vectors is associated with the magnitude of the incommensurate potential. The considerably large interlayer transfer integral and three-dimensional superconducting properties are due to the direct donor–donor interactions coming from the characteristic corrugated conducting sheet structure. The materials with high superconducting transition temperature, Tc, have large ratios of the observed cyclotron masses to the bare ones, which indicates that the strength of the many-body effect is the major determinant of Tc. (MDT-TS(AuI20.441 shows a metal–insulator transition at TMI=50 K, where MDT-TS is 5H-2-(1,3-diselenol-2-ylidene-1,3,4,6-tetrathiapentalene, and the insulating phase is an antiferromagnet with a high Néel temperature (TN=50 K and a high spin–flop field (Bsf=6.9 T. There is a possibility that this material is an incommensurate Mott insulator. Hydrostatic pressure suppresses the insulating state and induces superconductivity at Tc=3.2 K above 1.05 GPa, where Tc rises to the maximum, Tcmax=4.9 K at 1.27 GPa. This compound shows a usual temperature–pressure phase diagram, in which the superconducting phase borders on the antiferromagnetic insulating phase, despite the unusual band filling.

  16. 454-Pyrosequencing reveals variable fungal diversity across farming systems

    Directory of Open Access Journals (Sweden)

    Elham Ahmed Kazerooni

    2016-03-01

    Full Text Available Oasis farming system is common in some parts of the world, especially in the Arabian Peninsula and several African countries. In Oman, the farming system in the majority of farms follows a semi-oasis farming system, which is characterized by growing multiple crops mainly for home consumption, but also for local market. This study was conducted to investigate fungal diversity using pyrosequencing approach in soils from a farm utilizing a semi-oasis farming system (SOF which is cultivated with date palms, acid limes and cucumbers. Fungal diversity from this farm was compared to that from an organic farm (OR growing cucumbers and tomatoes. Fungal diversity was found to be variable among different crops in the same farm. The observed OTUs, Chao1 richness estimates and Shannon diversity values indicated that soils from date palms and acid limes have higher fungal diversity compared to soil from cucumbers (SOF. In addition, they also indicated that the level of fungal diversity is higher in the rhizosphere of cucumbers grown in OR compared to SOF. Ascomycota was the most dominant phylum in most of the samples from the OR and SOF farms. Other dominant phyla are Microsporidia, Chytridiomycota and Basidiomycota. The differential level of fungal diversity within the SOF could be related to the variation in the cultural practices employed for each crop.

  17. Lexical and constructional organization of argument structure: a contrastive analysis

    DEFF Research Database (Denmark)

    Pedersen, Johan

    2009-01-01

    exclusive focus on lexicalization patterns. Contrastive analysis may provide insight into differing ways of organizing grammatical information. Construction grammar (CXG) suggests that clausal core information is organized by integrating at least two construction types: A) schematic constructions, B...... of constructional specificity at which the core information is organized. English (and presumably other Germanic languages to some extent) tends to organize principal clausal information in schematic argument structure constructions, lea­ving secondary information for lexical (verbal) specification. Spanish (and...... presumably other Romance languages to some extent) seems to organize principal clausal information lexically in verbal argument structure constructions, leaving secondary information for schematically organized specification....

  18. Organizations and the Media: Structures of Miscommunication.

    Science.gov (United States)

    Theus, Kathryn T.

    1993-01-01

    Surveys 140 randomly selected profit and nonprofit organizations covered in 7 newspapers, and interviews journalists and organizational respondents. Finds that systematic discrepancies between organizations and reporters on the salience, selection, and interpretation of news reports were more common for public sector mechanistic bureaucracies of…

  19. STRUCTURE OF WAVE FRONT AND ORGANIZATION CENTER IN EXCITABLE MEDIA

    Institute of Scientific and Technical Information of China (English)

    刘深泉

    2004-01-01

    With help of establishing the moving coordinate on the wave front surface and the perturbation analysis in the boundary layer, the structures of wave front and organization center in excitable media were studied. The eikonal equation of wave front surface and general equation of organization center were obtained. These eikonal equations reveal the wave front surfaces have structures of twisted scroll wave and Mobius band, the organization centers have structures of knotted and linked ring. These theoretical results not only explain the wave patterns of BZ ( Belousov-Zhabotinskii ) chemical reaction but also give several possibility structures of wave front surface and organization center in general excitable media.

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

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

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

  1. Metal Organic Frameworks: From Structure to Property

    OpenAIRE

    Bu, Fei

    2016-01-01

    Porous Materials are an important class of materials due to their large-scale industrial applications in gas adsorption, gas separation, heterogeneous catalysis and so on. Among many kinds of porous materials, metal organic frameworks (MOFs) have emerged as one of the favorites in the past fifteen years. MOFs are crystalline porous materials that are mainly made of inorganic metal containing units (secondary building units, also called SBUs), organic ligands and templates.Compared to commerci...

  2. Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.

    Directory of Open Access Journals (Sweden)

    Jiyoung Ahn

    Full Text Available OBJECTIVES: The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. METHODS: Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp. Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM. Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. RESULTS: The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86. 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84. CONCLUSION: Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.

  3. 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...

  4. Structural Barriers: Redesigning Schools to Create Learning Organizations

    Science.gov (United States)

    Randeree, Ebrahim

    2006-01-01

    Purpose: The purpose of this paper is to focus on schools and address the structural dimensions of the organization as well as the hierarchical design of information flows between stakeholders. The paper highlights current structural barriers to creating learning organizations. Design/methodology/approach: This paper utilizes a conceptual model.…

  5. Structural Capability of an Organization toward Innovation Capability

    DEFF Research Database (Denmark)

    Nielsen, Susanne Balslev; Momeni, Mostafa

    2016-01-01

    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...... of innovation capability and proposes a conceptual framework based on a Qualitative Meta Synthesis of academic literature on organizations innovation capability. This is proposed for the development of the concept of innovation capability in the organizations and this paper includes an expert based validation...... Capability and Structural Capability. Also, it offers the most important components and indices which directly influence and are related to the structural capability of innovation capability....

  6. 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.

  7. Structure and organization of primary care.

    NARCIS (Netherlands)

    Lember, M.; Cartier, T.; Bourgueil, Y.; Dedeu, T.; Hutchinson, A.; Kringos, D.

    2015-01-01

    The way primary care is structured establishes important conditions for both the process of care and its outcomes. In this chapter, the structure of primary care will be discussed according to three dimensions: governance, economic conditions and workforce development. Governance refers to the visi

  8. Structure and organization of primary care.

    NARCIS (Netherlands)

    Lember, M.; Cartier, T.; Bourgueil, Y.; Dedeu, T.; Hutchinson, A.; Kringos, D.

    2015-01-01

    The way primary care is structured establishes important conditions for both the process of care and its outcomes. In this chapter, the structure of primary care will be discussed according to three dimensions: governance, economic conditions and workforce development. Governance refers to the

  9. The Temporal Organization of Syllabic Structure

    Science.gov (United States)

    Shaw, Jason A.

    2010-01-01

    This dissertation develops analytical tools which enable rigorous evaluation of competing syllabic parses on the basis of temporal patterns in speech production data. The data come from the articulographic tracking of fleshpoints on target speech organs, e.g., tongue, lips, jaw, in experiments with native speakers of American English and Moroccan…

  10. PLAN FOR PERFORMANCE ADMINISTRATION IN PYRAMIDAL STRUCTURE ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    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.

  11. [Classification of organisms and structuralism in biology].

    Science.gov (United States)

    Vasil'eva, L I

    2001-01-01

    Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

  12. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments.

    Science.gov (United States)

    Chaudhry, Vasvi; Rehman, Ateequr; Mishra, Aradhana; Chauhan, Puneet Singh; Nautiyal, Chandra Shekhar

    2012-08-01

    Community level physiological profiling and pyrosequencing-based analysis of the V1-V2 16S rRNA gene region were used to characterize and compare microbial community structure, diversity, and bacterial phylogeny from soils of chemically cultivated land (CCL), organically cultivated land (OCL), and fallow grass land (FGL) for 16 years and were under three different land use types. The entire dataset comprised of 16,608 good-quality sequences (CCL, 6,379; OCL, 4,835; FGL, 5,394); among them 12,606 sequences could be classified in 15 known phylum. The most abundant phylum were Proteobacteria (29.8%), Acidobacteria (22.6%), Actinobacteria (11.1%), and Bacteroidetes (4.7%), while 24.3% of the sequences were from bacterial domain but could not be further classified to any known phylum. Proteobacteria, Bacteroidetes, and Gemmatimonadetes were found to be significantly abundant in OCL soil. On the contrary, Actinobacteria and Acidobacteria were significantly abundant in CCL and FGL, respectively. Our findings supported the view that organic compost amendment (OCL) activates diverse group of microorganisms as compared with conventionally used synthetic chemical fertilizers. Functional diversity and evenness based on carbon source utilization pattern was significantly higher in OCL as compared to CCL and FGL, suggesting an improvement in soil quality. This abundance of microbes possibly leads to the enhanced level of soil organic carbon, soil organic nitrogen, and microbial biomass in OCL and FGL soils as collated with CCL. This work increases our current understanding on the effect of long-term organic and chemical amendment applications on abundance, diversity, and composition of bacterial community inhabiting the soil for the prospects of agricultural yield and quantity of soil.

  13. Pyrosequencing: applicability for studying DNA damage-induced mutagenesis.

    Science.gov (United States)

    Minko, Irina G; Earley, Lauriel F; Larlee, Kimberly E; Lin, Ying-Chih; Lloyd, R Stephen

    2014-10-01

    Site-specifically modified DNAs are routinely used in the study of DNA damage-induced mutagenesis. These analyses involve the creation of DNA vectors containing a lesion at a pre-determined position, DNA replication, and detection of mutations at the target site. The final step has previously required the isolation of individual DNA clones, hybridization with radioactively labeled probes, and verification of mutations by Sanger sequencing. In the search for an alternative procedure that would allow direct quantification of sequence variants in a mixed population of DNA molecules, we evaluated the applicability of pyrosequencing to site-specific mutagenesis assays. The progeny DNAs were analyzed that originated from replication of N(6) -(deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dG)-containing vectors in primate cells, with the lesion being positioned in the 5'-GCNGG-3' sequence context. Pyrosequencing detected ∼8% G to T transversions and ∼3.5% G to A transitions, a result that was in excellent agreement with frequencies previously measured by the standard procedure (Earley LF et al. [2013]: Chem Res Toxicol 26:1108-1114). However, ∼3.5% G to C transversions and ∼2.0% deletions could not be detected by pyrosequencing. Consistent with these observations, the sensitivity of pyrosequencing for measuring the single deoxynucleotide variants differed depending on the deoxynucleotide identity, and in the given sequence contexts, was determined to be ∼1-2% for A and T and ∼5% for C. Pyrosequencing of other DNA isolates that were obtained following replication of MeFapy-dG-containing vectors in primate cells or Escherichia coli, identified several additional limitations. Collectively, our data demonstrated that pyrosequencing can be used for studying DNA damage-induced mutagenesis as an effective complementary experimental approach to current protocols.

  14. Technology and structure of nursing organizations.

    Science.gov (United States)

    Alexander, J W; Mark, B

    1990-04-01

    Theory building and theory application in nursing administration enable the nurse executive to work more effectively at the managerial task. Alexander and Mark apply a model that allows for comparison and contrast between various nursing units based on the nature of their work as assessed on the variables of technology and structure. In this model, technology is assessed on three dimensions: instability, variability, and uncertainty; and structure is assessed as to vertical participation, horizontal participation, and formalization. Cases studies clarify the model and show its application.

  15. Evolution of bacterial diversity during two-phase olive mill waste ("alperujo") composting by 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Tortosa, Germán; Castellano-Hinojosa, Antonio; Correa-Galeote, David; Bedmar, Eulogio J

    2017-01-01

    Microorganisms are the main contributing factor responsible for organic matter degradation during composting. In this research, the 454-pyrosequencing of the 16S rRNA gene was used to elucidate evolution of bacterial diversity during mesophilic, thermophilic and maturation composting stages of the two-phase olive mill waste ("alperujo"), the main by-product of the Spanish olive oil industry. Two similar piles were performance composting AL with sheep manure as bulking agent. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the main phyla found in genomic libraries from each composting phase. Shannon and Chao1 biodiversity indices showed a clear difference between the mesophilic/thermophilic and maturation phases, which was mainly due to detection of new genera. PCA analysis of the relative number of sequences confirmed maturation affected bacterial population structure, and Pearson correlation coefficients between physicochemical composting parameters and relative number of genera sequences suggest that Planomicrobium and Ohtaekwangia could be considered as biomarkers for AL composting maturation.

  16. Fluctuating structure of aqueous organic nanodroplets

    Science.gov (United States)

    Hrahsheh, Fawaz; Wilemski, Gerald

    2013-05-01

    Supercooled and nano-confined water occurs frequently as nanometer-sized aqueousorganic aerosol droplets that are ubiquitous in the atmosphere and in many industrial processes. Nanodroplet structure is important because it influences droplet growth and evaporation rates, heterogeneous reaction rates, and radiative properties. We used classical molecular dynamic simulations to study the structure of binary water-nonane and ternary water-butanol-nonane nanodroplets for several temperatures and droplet sizes. We found that nonspherical, phase-separated Russian Doll (RD) structures occur for water/nonane nanodroplets at all temperatures studied, 220K-300K. The RD structure consists of a nearly spherical water droplet partially wetted by a convex lens of nonane. We then studied the effects of butanol on the wetting of the water/butanol core-shell droplet by the nonane lens. At low concentrations, butanol acts as a surfactant to significantly enhance the wetability of the water droplet by nonane. At 250 K, with sufficient butanol and nonane, perfect wetting (thin film formation by nonane) occurs. Perfect wetting also occurs at higher temperatures, 270 K to 300 K, but this wetting state is progressively destabilized at higher temperature. All of the nanodroplets studied undergo distinct transitions between partial dewetting and perfect wetting states due to isothermal fluctuations in the local distribution of butanol on the surface of the water core. These fluctuations favor the wetted state at lower temperatures and the dewetted state at higher temperatures.

  17. Simulating Self-organization and Interference between Certain Hierarchical Structures.

    Science.gov (United States)

    Raczynski, Stanislaw

    2014-10-01

    A model of the dynamics and interactions between organizations with self-organizing hierarchical structures is presented for discrete events. The active objects of the model are individuals (people, organization members). The parameters of an individual are ability, corruption level, resources, and lust for power, among others. Three organizations are generated and interact with each other, attempting to gain more members and power. The individuals appear and disappear, due to a simple 'birth-and-death' process. If an individual disappears from the model, a corresponding reconfiguration in the hierarchical structure occurs. The organization's growth and macro-patterns are the result of the activities of the individuals. The aim of the simulation is to visualize the evolution of the organizations and the stability of the whole system. A 'steady state' for the model is rare; instead, in most parameter configurations, the model enters into oscillations.

  18. Structure and organization of heteromeric AMPA-type glutamate receptors

    National Research Council Canada - National Science Library

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

    2016-01-01

    .... 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...

  19. Detection of MGMT promoter methylation in glioblastoma using pyrosequencing.

    Science.gov (United States)

    Xie, Hao; Tubbs, Raymond; Yang, Bin

    2015-01-01

    Recent clinical trials on patients with glioblastoma revealed that O6-Methylguanine-DNA methyltransferase (MGMT) methylation status significantly predicts patient's response to alkylating agents. In this study, we sought to develop and validate a quantitative MGMT methylation assay using pyrosequencing on glioblastoma. We quantified promoter methylation of MGMT using pyrosequencing on paraffin-embedded fine needle aspiration biopsy tissues from 43 glioblastoma. Using a 10% cutoff, MGMT methylation was identified in 37% cases of glioblastoma and 0% of the non-neoplastic epileptic tissue. Methylation of any individual CpG island in MGMT promoter ranged between 33% and 95%, with a mean of 65%. By a serial dilution of genomic DNA of a homogenously methylated cancer cell line with an unmethylated cell line, the analytical sensitivity is at 5% for pyrosequencing to detect MGMT methylation. The minimal amount of genomic DNA required is 100 ng (approximately 3,000 cells) in small fine needle biopsy specimens. Compared with methylation-specific PCR, pyrosequencing is comparably sensitive, relatively specific, and also provides quantitative information for each CpG methylation.

  20. Rapid identification of nine species of diphyllobothriidean tapeworms by pyrosequencing

    Science.gov (United States)

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

    2016-01-01

    The identification of diphyllobothriidean tapeworms (Cestoda: Diphyllobothriidea) that infect humans and intermediate/paratenic hosts is extremely difficult due to their morphological similarities, particularly in the case of Diphyllobothrium and Spirometra species. A pyrosequencing method for the molecular identification of pathogenic agents has recently been developed, but as of yet there have been no reports of pyrosequencing approaches that are able to discriminate among diphyllobothriidean species. This study, therefore, set out to establish a pyrosequencing method for differentiating among nine diphyllobothriidean species, Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium latum, Diphyllobothrium nihonkaiense, Diphyllobothrium stemmacephalum, Diplogonoporus balaenopterae, Adenocephalus pacificus, Spirometra decipiens and Sparganum proliferum, based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as a molecular marker. A region of 41 nucleotides in the cox1 gene served as a target, and variations in this region were used for identification using PCR plus pyrosequencing. This region contains nucleotide variations at 12 positions, which is enough for the identification of the selected nine species of diphyllobothriidean tapeworms. This method was found to be a reliable tool not only for species identification of diphyllobothriids, but also for epidemiological studies of cestodiasis caused by diphyllobothriidean tapeworms at public health units in endemic areas. PMID:27853295

  1. Pyrosequencing reveals bacteria carried in different wind eroded sediments

    Science.gov (United States)

    Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. A novel technique, pyrosequencing, promises to expand our understanding of the vast microbial diversity of soils and eroded sediments as it can sequence between 10-10...

  2. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway

    OpenAIRE

    Grishin, Andrey M.; Miroslaw Cygler

    2015-01-01

    Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compo...

  3. Structural organization of the mitochondrial respiratory chain.

    Science.gov (United States)

    Genova, Maria Luisa; Bianchi, Cristina; Lenaz, Giorgio

    2003-03-01

    Two models exist of the mitochondrial respiratory chain: the model of a random organization of the individual respiratory enzyme complexes and that of a super-complex assembly formed by stable association between the individual complexes. Recently Schägger, using digitonin solubilization and Blue Native PAGE produced new evidence of preferential associations, in particular a Complex I monomer with a Complex III dimer, and suggested a model of the respiratory chain (the respirasome) based on direct electron channelling between complexes. Discrimination between the two models is amenable to kinetic testing using flux control analysis. Experimental evidence obtained in beef heart SMP, according to the extension of the Metabolic Control Theory for pathways with metabolic channelling, showed that enzyme associations involving Complex I and Complex III take place in the respiratory chain while Complex IV seems to be randomly distributed, with cytochrome c behaving as a mobile component. Flux control analysis at anyone of the respiratory complexes involved in aerobic succinate oxidation indicated that Complex II and III are not functionally associated in a stable supercomplex. A critical appraisal of the solid-state model of the mitochondrial respiratory chain requires its reconciliation with previous biophysical and kinetic evidence that CoQ behaves as a homogeneous diffusible pool between all reducing enzyme and all oxidizing enzymes: the hypothesis can be advanced that both models (CoQ pool and supercomplexes) are true, by postulating that supercomplexes physiologically exist in equilibrium with isolated complexes depending on metabolic conditions of the cell.

  4. The structure and function of auditory chordotonal organs in insects.

    Science.gov (United States)

    Yack, Jayne E

    2004-04-15

    Insects are capable of detecting a broad range of acoustic signals transmitted through air, water, or solids. Auditory sensory organs are morphologically diverse with respect to their body location, accessory structures, and number of sensilla, but remarkably uniform in that most are innervated by chordotonal organs. Chordotonal organs are structurally complex Type I mechanoreceptors that are distributed throughout the insect body and function to detect a wide range of mechanical stimuli, from gross motor movements to air-borne sounds. At present, little is known about how chordotonal organs in general function to convert mechanical stimuli to nerve impulses, and our limited understanding of this process represents one of the major challenges to the study of insect auditory systems today. This report reviews the literature on chordotonal organs innervating insect ears, with the broad intention of uncovering some common structural specializations of peripheral auditory systems, and identifying new avenues for research. A general overview of chordotonal organ ultrastructure is presented, followed by a summary of the current theories on mechanical coupling and transduction in monodynal, mononematic, Type 1 scolopidia, which characteristically innervate insect ears. Auditory organs of different insect taxa are reviewed, focusing primarily on tympanal organs, and with some consideration to Johnston's and subgenual organs. It is widely accepted that insect hearing organs evolved from pre-existing proprioceptive chordotonal organs. In addition to certain non-neural adaptations for hearing, such as tracheal expansion and cuticular thinning, the chordotonal organs themselves may have intrinsic specializations for sound reception and transduction, and these are discussed. In the future, an integrated approach, using traditional anatomical and physiological techniques in combination with new methodologies in immunohistochemistry, genetics, and biophysics, will assist in

  5. Quality score based identification and correction of pyrosequencing errors.

    Science.gov (United States)

    Iyer, Shyamala; Bouzek, Heather; Deng, Wenjie; Larsen, Brendan; Casey, Eleanor; Mullins, James I

    2013-01-01

    Massively-parallel DNA sequencing using the 454/pyrosequencing platform allows in-depth probing of diverse sequence populations, such as within an HIV-1 infected individual. Analysis of this sequence data, however, remains challenging due to the shorter read lengths relative to that obtained by Sanger sequencing as well as errors introduced during DNA template amplification and during pyrosequencing. The ability to distinguish real variation from pyrosequencing errors with high sensitivity and specificity is crucial to interpreting sequence data. We introduce a new algorithm, CorQ (Correction through Quality), which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. We tested the ability of CorQ to correctly call SNPs on a set of pyrosequences derived from ten viral genomes from an HIV-1 infected individual, as well as on six simulated pyrosequencing datasets generated using non-zero error rates to emulate errors introduced by PCR. When combined with the AmpliconNoise error correction method developed to remove ambiguities in signal intensities, we attained a 97% reduction in indel errors, a 98% reduction in carry forward errors, and >97% specificity of SNP detection. When compared to four other error correction methods, AmpliconNoise+CorQ performed at equal or higher SNP identification specificity, but the sensitivity of SNP detection was consistently higher (>98%) than other methods tested. This combined procedure will therefore permit examination of complex genetic populations with improved accuracy.

  6. Structural organization of DNA in chlorella viruses.

    Directory of Open Access Journals (Sweden)

    Timo Wulfmeyer

    Full Text Available Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm(-3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.

  7. The Structural and Functional Organization of Cognition.

    Science.gov (United States)

    Snow, Peter J

    2016-01-01

    This article proposes that what have been historically and contemporarily defined as different domains of human cognition are served by one of four functionally- and structurally-distinct areas of the prefrontal cortex (PFC). Their contributions to human intelligence are as follows: (a) BA9, enables our emotional intelligence, engaging the psychosocial domain; (b) BA47, enables our practical intelligence, engaging the material domain; (c) BA46 (or BA46-9/46), enables our abstract intelligence, engaging the hypothetical domain; and (d) BA10, enables our temporal intelligence, engaging in planning within any of the other three domains. Given their unique contribution to human cognition, it is proposed that these areas be called the, social (BA9), material (BA47), abstract (BA46-9/46) and temporal (BA10) mind. The evidence that BA47 participates strongly in verbal and gestural communication suggests that language evolved primarily as a consequence of the extreme selective pressure for practicality; an observation supported by the functional connectivity between BA47 and orbital areas that negatively reinforce lying. It is further proposed that the abstract mind (BA46-9/46) is the primary seat of metacognition charged with creating adaptive behavioral strategies by generating higher-order concepts (hypotheses) from lower-order concepts originating from the other three domains of cognition.

  8. Polymeric Thin Films for Organic Electronics: Properties and Adaptive Structures

    Directory of Open Access Journals (Sweden)

    Bruno Pignataro

    2013-03-01

    Full Text Available This review deals with the correlation between morphology, structure and performance of organic electronic devices including thin film transistors and solar cells. In particular, we report on solution processed devices going into the role of the 3D supramolecular organization in determining their electronic properties. A selection of case studies from recent literature are reviewed, relying on solution methods for organic thin-film deposition which allow fine control of the supramolecular aggregation of polymers confined at surfaces in nanoscopic layers. A special focus is given to issues exploiting morphological structures stemming from the intrinsic polymeric dynamic adaptation under non-equilibrium conditions.

  9. Principles of disaster management lesson. 12: structuring organizations.

    Science.gov (United States)

    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.

  10. 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.

  11. Tritium labeling of organic compounds deposited on porous structures

    Science.gov (United States)

    Ehrenkaufer, Richard L. E.; Wolf, Alfred P.; Hembree, Wylie C.

    1979-01-01

    An improved process for labeling organic compounds with tritium is carried out by depositing the selected compound on the extensive surface of a porous structure such as a membrane filter and exposing the membrane containing the compound to tritium gas activated by the microwave discharge technique. The labeled compound is then recovered from the porous structure.

  12. Self-organization and coherent structures in plasmas and fluids

    DEFF Research Database (Denmark)

    Nielsen, A.H.; Juul Rasmussen, J.; Schmidt, M.R.

    1996-01-01

    momentum the development into propagating dipolar structures is observed. This development is discussed by employing self-organization principles. The detailed structures of the evolving dipoles depends on the initial condition. It seems that there are no unique dipolar solutions, but a large class...

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

    Directory of Open Access Journals (Sweden)

    Robert J Boissy

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

  14. Functional and structural microbial diversity in organic and conventional viticulture: organic farming benefits natural biocontrol agents.

    Science.gov (United States)

    Schmid, Florian; Moser, Gerit; Müller, Henry; Berg, Gabriele

    2011-03-01

    Statistically significant differences in the structure and function of above-ground grapevine-associated microorganisms from organically and conventionally managed vineyards were found. Aureobasidium pullulans, a copper-detoxifying fungus and biocontrol agent, plays a key role in explaining these differences. The black fungus was strongly enriched in the communities of organically managed plants and yielded a higher indigenous antiphytopathogenic potential.

  15. 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.

  16. Pyrosequencing reveals the key microorganisms involved in sludge alkaline fermentation for efficient short-chain fatty acids production.

    Science.gov (United States)

    Zheng, Xiong; Su, Yinglong; Li, Xiang; Xiao, Naidong; Wang, Dongbo; Chen, Yinguang

    2013-05-07

    Short-chain fatty acids (SCFAs) have been regarded as the excellent carbon source of wastewater biological nutrient removal, and sludge alkaline (pH 10) fermentation has been reported to achieve highly efficient SCFAs production. In this study, the underlying mechanisms for the improved SCFAs production at pH 10 were investigated by using 454 pyrosequencing and fluorescent in situ hybridization (FISH) to analyze the microbial community structures in sludge fermentation reactors. It was found that sludge fermentation at pH 10 increased the abundances of Pseudomonas sp. and Alcaligenes sp., which were able to excrete extracellular proteases and depolymerases, and thus enhanced the hydrolysis of insoluble sludge protein and polyhydroxyalkanoates (PHA). Meanwhile, the abundance of acid-producing bacteria (such as Clostridium sp.) in the reactor of pH 10 was also higher than that of uncontrolled pH, which benefited the acidification of soluble organic substrates. Further study indicated that sludge fermentation at pH 10 significantly decreased the number of methanogenic archaea, resulting in lower SCFAs consumption and lower methane production. Therefore, anaerobic sludge fermentation under alkaline conditions increased the abundances of bacteria involved in sludge hydrolysis and acidification, and decreased the abundance of methanogenic archaea, which favored the competition of bacteria over methanogens and resulted in the efficient production of SCFAs.

  17. 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.

  18. Pyrosequencing-based assessment of microbial community shifts in leachate from animal carcass burial lysimeter.

    Science.gov (United States)

    Kim, Hyun Young; Seo, Jiyoung; Kim, Tae-Hun; Shim, Bomi; Cha, Seok Mun; Yu, Seungho

    2017-02-26

    This study examined the use of microbial community structure as a bio-indicator of decomposition levels. High-throughput pyrosequencing technology was used to assess the shift in microbial community of leachate from animal carcass lysimeter. The leachate samples were collected monthly for one year and a total of 164,639 pyrosequencing reads were obtained and used in the taxonomic classification and operational taxonomy units (OTUs) distribution analysis based on sequence similarity. Our results show considerable changes in the phylum-level bacterial composition, suggesting that the microbial community is a sensitive parameter affected by the burial environment. The phylum classification results showed that Proteobacteria (Pseudomonas) were the most influential taxa in earlier decomposition stage whereas Firmicutes (Clostridium, Sporanaerobacter, and Peptostreptococcus) were dominant in later stage under anaerobic conditions. The result of this study can provide useful information on a time series of leachate profiles of microbial community structures and suggest patterns of microbial diversity in livestock burial sites. In addition, this result can be applicable to predict the decomposition stages under clay loam based soil conditions of animal livestock.

  19. 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.

  20. 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.

  1. Additive Manufacturing of Biomedical Constructs with Biomimetic Structural Organizations

    OpenAIRE

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

    2016-01-01

    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, dep...

  2. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing.

    Science.gov (United States)

    Logares, Ramiro; Audic, Stephane; Santini, Sebastien; Pernice, Massimo C; de Vargas, Colomban; Massana, Ramon

    2012-10-01

    Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter '454') allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (∼2-5 μm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellates.

  3. Pyrosequencing reveals microbial community profile in anaerobic bio-entrapped membrane reactor for pharmaceutical wastewater treatment.

    Science.gov (United States)

    Ng, Kok Kwang; Shi, Xueqing; Ong, Say Leong; Ng, How Yong

    2016-01-01

    In this study, pharmaceutical wastewater with high salinity and total chemical oxygen demand (TCOD) was treated by an anaerobic membrane bioreactor (AnMBR) and an anaerobic bio-entrapped membrane reactor (AnBEMR). The microbial populations and communities were analyzed using the 454 pyrosequencing method. The hydraulic retention time (HRT), membrane flux and mean cell residence time (MCRT) were controlled at 30.6h, 6L/m(2)h and 100d, respectively. The results showed that the AnBEMR achieved higher TCOD removal efficiency and greater biogas production compared to the AnMBR. Through DNA pyrosequencing analysis, both the anaerobic MBRs showed similar dominant groups of bacteria and archaea. However, phylum Elusimicrobia of bacteria was only detected in the AnBEMR; the higher abundance of dominant archaeal genus Methanimicrococcus found in the AnBEMR could play an important role in degradation of the major organic pollutant (i.e., trimethylamine) present in the pharmaceutical wastewater. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Discovery of Single Nucleotide Polymorphisms and Mutations by Pyrosequencing

    OpenAIRE

    2006-01-01

    Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how t...

  6. Allele-Specific DNA Methylation Detection by Pyrosequencing®

    DEFF Research Database (Denmark)

    Sommer Kristensen, Lasse; 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....

  7. The ascidian pigmented sensory organs: structures and developmental programs.

    Science.gov (United States)

    Esposito, R; Racioppi, C; Pezzotti, M R; Branno, M; Locascio, A; Ristoratore, F; Spagnuolo, A

    2015-01-01

    The recent advances on ascidian pigment sensory organ development and function represent a fascinating platform to get insight on the basic programs of chordate eye formation. This review aims to summarize current knowledge, at the structural and molecular levels, on the two main building blocks of ascidian light sensory organ, i.e. pigment cells and photoreceptor cells. The unique features of these structures (e.g., simplicity and well characterized cell lineage) are indeed making it possible to dissect the developmental programs at single cell resolution and will soon provide a panel of molecular tools to be exploited for a deep developmental and comparative-evolutionary analysis.

  8. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    Directory of Open Access Journals (Sweden)

    Farmerie William G

    2006-08-01

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

  9. Structure-Function Relationships in Semiconducting Polymers for Organic Photovoltaics

    OpenAIRE

    Kavulak, David Fredric Joel

    2010-01-01

    The major body of this work investigates how the chemical structure of conjugated polymers relates to the fundamental operating mechanism of organic photovoltaic devices. New conjugated polymers were characterized and their optical and electronic properties tested and correlated with their power conversion efficiencies as the active layer in polymer solar cells. From these experiments general structure/function relationships are drawn with an eye toward developing universal guidelines for con...

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

    Directory of Open Access Journals (Sweden)

    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

  11. Stochastic models for plant microtubule self-organization and structure.

    Science.gov (United States)

    Eren, Ezgi C; Dixit, Ram; Gautam, Natarajan

    2015-12-01

    One of the key enablers of shape and growth in plant cells is the cortical microtubule (CMT) system, which is a polymer array that forms an appropriately-structured scaffolding in each cell. Plant biologists have shown that stochastic dynamics and simple rules of interactions between CMTs can lead to a coaligned CMT array structure. However, the mechanisms and conditions that cause CMT arrays to become organized are not well understood. It is prohibitively time-consuming to use actual plants to study the effect of various genetic mutations and environmental conditions on CMT self-organization. In fact, even computer simulations with multiple replications are not fast enough due to the spatio-temporal complexity of the system. To redress this shortcoming, we develop analytical models and methods for expeditiously computing CMT system metrics that are related to self-organization and array structure. In particular, we formulate a mean-field model to derive sufficient conditions for the organization to occur. We show that growth-prone dynamics itself is sufficient to lead to organization in presence of interactions in the system. In addition, for such systems, we develop predictive methods for estimation of system metrics such as expected average length and number of CMTs over time, using a stochastic fluid-flow model, transient analysis, and approximation algorithms tailored to our problem. We illustrate the effectiveness of our approach through numerical test instances and discuss biological insights.

  12. Structural and electronic implications for carrier injection into organic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Castellani, Mauro [Universitaet Potsdam, Institut fuer Physik und Astronomie, Potsdam-Golm (Germany); Salzmann, Ingo; Yu, Shuwen; Koch, Norbert [Humboldt-Universitaet zu Berlin, Institut fuer Physik, Berlin (Germany); Bugnon, Philippe [Ecole Polytechnique Federale de Lausanne (Switzerland). Institut des Materiaux; Oehzelt, Martin [Johannes Kepler Universitaet Linz (Austria). Institut fuer Experimentalphysik

    2009-10-15

    We report on the structural and electronic interface formation between ITO (indium-tin-oxide) and prototypical organic small molecular semiconductors, i.e., CuPc (copper phthalocyanine) and {alpha}-NPD (N,N'-di(naphtalen-1-yl)-N,N'-diphenyl-benzidine). In particular, the effects of in situ oxygen plasma pretreatment of the ITO surface on interface properties are examined in detail: Organic layer-thickness dependent Kelvin probe measurements revealed a good alignment of the ITO work function and the highest occupied electronic level of the organic material in all samples. In contrast, the electrical properties of hole-only and bipolar organic diodes depend strongly on the treatment of ITO prior to organic deposition. This dependence is more pronounced for diodes made of polycrystalline CuPc than for those of amorphous {alpha}-NPD layers. X-ray diffraction and atomic force microscopic (AFM) investigations of CuPc nucleation and growth evidenced a more pronounced texture of the polycrystalline film structure on the ITO substrate that was oxygen plasma treated prior to organic layer deposition. These findings suggest that the anisotropic electrical properties of CuPc crystallites, and their orientation with respect to the substrate, strongly affect the charge carrier injection and transport properties at the anode interface. (orig.)

  13. Demand structure and willingness to pay for organic dairy products

    DEFF Research Database (Denmark)

    Smed, Sinne

    2005-01-01

    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...

  14. Consumer knowledge structures with regards to organic foods

    DEFF Research Database (Denmark)

    Bredahl, Lone; Thøgersen, John; Dean, Moira

    2004-01-01

    ; through hierarchical value maps and through perceptual maps derived from correspondence analyses, both across stimuli. Results point to marked differences in knowledge structures concerning organic foods among consumer segments, both at product-knowledge level and at self-knowledge level. The exact values...

  15. Twelve Tips for Organizing an Objective Structured Clinical Examination (OSCE).

    Science.gov (United States)

    Harden, R. M.

    1991-01-01

    Suggestions for organizing the objective structured clinical examination for medical students and physicians address selection of competencies to be evaluated, number, type, and duration of examination stations, use of examiners, clarity of instructions, test administration, resource requirements, interstation signals, and recordkeeping. (MSE)

  16. Effects of Discourse Structure Graphic Organizers on EFL Reading Comprehension

    Science.gov (United States)

    Jiang, Xiangying

    2012-01-01

    This study investigated the effects of a 16-week reading instruction program with discourse structure graphic organizers (DSGOs) on the development of English reading comprehension among college-level English as a Foreign Language (EFL) students. A total of 340 first and third semester students of non-English majors at a Chinese university…

  17. Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods.

    Science.gov (United States)

    Li, Ping; Jiang, Dawei; Li, Bing; Dai, Xinyue; Wang, Yanhong; Jiang, Zhou; Wang, Yanxin

    2014-12-01

    A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. 12 bacterial and 18 archaeal DGGE bands and 26-136 species-level OTUs were detected for all the samples. 299 bacterial and 283 archaeal 16S rRNA gene clones for two typical samples were identified by phylogenetic analysis. Most of the results from these different methods were consistent with the dominant bacterial populations. But the proportions of the microbial populations were mostly different and the bacterial communities in most of these samples from pyrosequencing were both more abundant and more diverse than those from the traditional methods. Even after quality filtering, pyrosequencing revealed some populations including Alishewanella, Sulfuricurvum, Arthrobacter, Sporosarcina and Algoriphagus which were not detected with traditional techniques. The most dominant bacterial populations in these samples identified as some arsenic, iron, nitrogen and sulfur reducing and oxidizing related populations including Acinetobacter, Pseudomonas, Flavobacterium, Brevundimonas, Massilia, Planococcus, and Aquabacterium and archaeal communities Nitrosophaera and Methanosaeta. Acinetobacter and Pseudomonas were distinctly abundant in most of these samples. Methanogens were found as the dominant archeal population with three methods. From the results of traditional methods, the dominant archaeal populations apparently changed from phylum Thaumarchaeota to Euryarchaeota with the arsenic concentrations increasing. But this structure dynamic change was not revealed with pyrosequencing. Our results imply that an integrated approach combining the traditional methods and next generation sequencing approaches to characterize the microbial communities in high arsenic groundwater is recommended.

  18. Self-organized structures in soft confined thin films

    Indian Academy of Sciences (India)

    Ashutosh Sharma

    2005-10-01

    We present a mini-review of our recent work on spontaneous, self-organized creation of mesostructures in soft materials like thin films of polymeric liquids and elastic solids. These very small scale, highly confined systems are inherently unstable and thus self-organize into ordered structures which can be exploited for MEMS, sensors, opto-electronic devices and a host of other nanotechnology applications. In particular, mesomechanics requires incorporation of intermolecular interactions and surface tension forces, which are usually inconsequential in classical macroscale mechanics. We point to some experiments and quasi-continuum simulations of self-organized structures in thin soft films which are germane not only to nanotechnology, but also to a spectrum of classical issues such as adhesion/debonding, wetting, coatings, tribology and membranes.

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

    Science.gov (United States)

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

    2014-05-01

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

  20. Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing.

    Science.gov (United States)

    Kaevska, Marija; Videnska, Petra; Sedlar, Karel; Slana, Iva

    2016-01-01

    The aims of this study were to determine the microbial community in five rivers in the proximity of a city in the Czech Republic using 454-pyrosequencing, as well as to assess seasonal variability over the course of 1 year and to identify the factors influencing the structure of bacterial communities. Samples from five rivers around the city of Brno were obtained during four seasons and analysed using 454 pyrosequencing of the 16S rRNA gene. The core composition of bacterial communities consisted of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, TM7 and others. Our approach enabled us to more closely study the correlation between the abundance of different families and environmental factors. Overall, Actinobacteria negatively correlated with phosphorus, sulphate, dissolved particle and chloride levels. In contrast, Proteobacteria positively correlated with sulphate, dissolved particle, chloride, dissolved oxygen and nitrite levels. Future work should focus on the dynamics of bacterial communities present in river water and their relation to the overall stability of the water ecosystem.

  1. Management, Organization, Structure. Theoretical Considerations and Empirical Evidence on Changes in the Management of Educational Organizations

    Directory of Open Access Journals (Sweden)

    Thorsten Peetz

    2010-09-01

    Full Text Available Based on a critique of rather narrow, economy-centered concepts of management, this article develops an alternative conceptualization that focuses on function-specific solutions to the problem of coordination in organizations. Drawing on Niklas LUHMANN's theory of organization we describe management in structural terms as related to organizational programs, channels of communication, persons and positions. We conclude by analyzing transformations of management in educational organizations and demonstrate how our re-conceptualization of management can be applied in empirical research. URN: urn:nbn:de:0114-fqs1003252

  2. Lexical and constructional organization of argument structure: a contrastive analysis

    DEFF Research Database (Denmark)

    Pedersen, Johan

    2009-01-01

    exclusive focus on lexicalization patterns. Contrastive analysis may provide insight into differing ways of organizing grammatical information. Construction grammar (CXG) suggests that clausal core information is organized by integrating at least two construction types: A) schematic constructions, B......) lexical constructions (e.g. Croft 2001; Fillmore 1988; Goldberg 1995, 2006). In addition, clausal expressions are, according to some CXG-frameworks (e.g. Croft 2001), supposed to be built on language-specific construction types. I hypothesize that languages may differ according to the level...... of constructional specificity at which the core information is organized. English (and presumably other Germanic languages to some extent) tends to organize principal clausal information in schematic argument structure constructions, lea­ving secondary information for lexical (verbal) specification. Spanish (and...

  3. PyroMark® Instruments, Chemistry, and Software for Pyrosequencing® Analysis.

    Science.gov (United States)

    Kreutz, Martin; Schock, Gerald; Kaiser, Julia; Hochstein, Norbert; Peist, Ralf

    2015-01-01

    Since the early 2000s, Pyrosequencing(®) technology has been adapted for various instrument platforms to enable users to examine the role of epigenetic DNA methylation in gene expression regulation, genetic markers for specific phenotypes in livestock, drug resistance development in pathogens, and polymorphisms in forensic samples of mitochondrial DNA.The instruments, software, and chemistry have been modified to facilitate different sample throughputs and sample amounts. Just recently, major changes have been implemented to enable increased read length and more precise Pyrosequencing results. These improvements were made possible through a number of changes to various system components. In addition, assay development has been streamlined through the availability of optimized PCR and Pyrosequencing reagents, automated assay design tools, and a number of predesigned Pyrosequencing assays.In future, instruments with smaller footprints and the ability to automate crucial steps of the Pyrosequencing protocol will be available and will provide even more convenient and standardized Pyrosequencing analysis with flexible throughput.

  4. ORGANIC VS CONVENTIONAL: SOIL NEMATODE COMMUNITY STRUCTURE AND FUNCTION.

    Science.gov (United States)

    Kapp, C; Storey, S G; Malan, A P

    2014-01-01

    Global increases in human population are creating an ever-greater need for food production. Poor soil management practices have degraded soil to such an extent that rapidly improved management practices is the only way to ensure future food demands. In South Africa, deciduous fruit producers are realising the need for soil health, and for an increased understanding of the benefits of soil ecology, to ensure sustainable fruit production. This depends heavily on improved orchard management. Conventional farming relies on the addition of artificial fertilizers, and the application of chemicals, to prevent or minimise, the effects of the soil stages of pest insects, and of plant-parasitic nematodes. Currently, there is resistance toward conventional farming practices, which, it is believed, diminishes biodiversity within the soil. The study aimed to establish the soil nematode community structure and function in organically, and conventionally, managed deciduous fruit orchards. This was done by determining the abundance, the diversity, and the functionality of the naturally occurring free-living, and plant-parasitic, nematodes in deciduous fruit orchards in the Western Cape province of South Africa. The objective of the study was to form the basis for the use of nematodes as future indicators of soil health in deciduous fruit orchards. Orchards from neighbouring organic, and conventional, apricot farms, and from an organic apple orchard, were studied. All the nematodes were quantified, and identified, to family level. The five nematode-classified trophic groups were found at each site, while 14 families were identified in each orchard, respectively. Herbivores were dominant in all the orchards surveyed. Organic apples had the fewest herbivores and fungivores, with the highest number of carnivores. When comparing organic with conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic apricot orchards. The Maturity Index (MI

  5. 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.

  6. 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.; Ball, William S.; Byars, Anna Weber; Schapiro, Mark; Bommer, Wendy; Carr, April; German, April; Dunn, Scott; Rivkin, Michael J.; Waber, Deborah; Mulkern, Robert; Vajapeyam, Sridhar; Chiverton, Abigail; Davis, Peter; Koo, Julie; Marmor, Jacki; Mrakotsky, Christine; Robertson, Richard; McAnulty, Gloria; Brandt, Michael E.; Fletcher, Jack M.; Kramer, Larry A.; Yang, Grace; McCormack, Cara; Hebert, Kathleen M.; Volero, Hilda; Botteron, Kelly; McKinstry, Robert C.; Warren, William; Nishino, Tomoyuki; Robert Almli, C.; Todd, Richard; Constantino, John; McCracken, James T.; Levitt, Jennifer; Alger, Jeffrey; O'Neil, Joseph; Toga, Arthur; Asarnow, Robert; Fadale, David; Heinichen, Laura; Ireland, Cedric; Wang, Dah-Jyuu; Moss, Edward; Zimmerman, Robert A.; Bintliff, Brooke; Bradford, Ruth; Newman, Janice; Evans, Alan C.; Arnaoutelis, Rozalia; Bruce Pike, G.; Louis Collins, D.; Leonard, Gabriel; Paus, Tomas; Zijdenbos, Alex; Das, Samir; Fonov, Vladimir; Fu, Luke; Harlap, Jonathan; Leppert, Ilana; Milovan, Denise; Vins, Dario; Zeffiro, Thomas; Van Meter, John; Lange, Nicholas; Froimowitz, Michael P.; Botteron, Kelly; Robert Almli, C.; Rainey, Cheryl; Henderson, Stan; Nishino, Tomoyuki; Warren, William; Edwards, Jennifer L.; Dubois, Diane; Smith, Karla; Singer, Tish; Wilber, Aaron A.; Pierpaoli, Carlo; Basser, Peter J.; Chang, Lin-Ching; Koay, Chen Guan; Walker, Lindsay; Freund, Lisa; Rumsey, Judith; Baskir, Lauren; Stanford, Laurence; Sirocco, Karen; Gwinn-Hardy, Katrina; Spinella, Giovanna; McCracken, James T.; Alger, Jeffry R.; Levitt, Jennifer; O'Neill, Joseph

    2013-01-01

    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. PMID:22784607

  7. Structure and Properties of an Amorphous Metal-Organic Framework

    Science.gov (United States)

    Bennett, Thomas D.; Goodwin, Andrew L.; Dove, Martin T.; Keen, David A.; Tucker, Matthew G.; Barney, Emma R.; Soper, Alan K.; Bithell, Erica G.; Tan, Jin-Chong; Cheetham, Anthony K.

    2010-03-01

    ZIF-4, a metal-organic framework (MOF) with a zeolitic structure, undergoes a crystal-amorphous transition on heating to 300°C. The amorphous form, which we term a-ZIF, is recoverable to ambient conditions or may be converted to a dense crystalline phase of the same composition by heating to 400°C. Neutron and x-ray total scattering data collected during the amorphization process are used as a basis for reverse Monte Carlo refinement of an atomistic model of the structure of a-ZIF. The structure is best understood in terms of a continuous random network analogous to that of a-SiO2. Optical microscopy, electron diffraction and nanoindentation measurements reveal a-ZIF to be an isotropic glasslike phase capable of plastic flow on its formation. Our results suggest an avenue for designing broad new families of amorphous and glasslike materials that exploit the chemical and structural diversity of MOFs.

  8. A pyrosequencing-based analysis of microbial diversity governed by ecological conditions in the Winogradsky column.

    Science.gov (United States)

    Abbasian, Firouz; Lockington, Robin; Mallavarapu, Megharaj; Naidu, Ravi

    2015-07-01

    The Winogradsky column is used as a microcosm to mimic both the microbial diversity and the ecological relationships between the organisms in lake sediments. In this study, a pyrosequencing approach was used to obtain a more complete list of the microbial organisms present in such columns and their ratios in different layers of this microcosm. Overall, 27 different phyla in these columns were detected in these columns, most (20 phyla) belonged to bacteria. Based on this study, Proteobacteria (mostly Sphingomonadales), Cyanobacteria (mostly Oscillatoriales) and Bacteroidetes (mostly Flavobacteriales) were the dominant microorganisms in the water, middle, and bottom layers of this column, respectively. Although the majority of organism in the water layer were photoautotrophic organisms, the ratio of the phototrophic organisms decreased in the lower layers, replaced by chemoheterotrophic bacteria. Furthermore, the proportion of aerobic chemoheterotrophic bacteria was greater in the higher layers of the column in comparison to the bottom. The green and purple sulfur phototrophic bacteria inhabited the bottom and middle of these columns, with none of them found in the water layer. Although the sulfur oxidizing bacteria were the dominant chemolithotrophic bacteria in the water layer, their ratio decreases in lower layers, being replaced with nitrogen oxidizing bacteria in the middle and bottom layers. Overall, the microbial population of these layers changes from a phototrophic and aerobic chemoheterotrophic organisms in the water layer to a mostly anaerobic chemoheterotrophic population of bacteria in the bottom layers.

  9. 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.

  10. Amelogenin sex determination by pyrosequencing of short PCR products.

    Science.gov (United States)

    Tschentscher, Frank; Frey, Ulrich H; Bajanowski, Thomas

    2008-07-01

    We developed an assay, which allows the sex determination of human DNA samples by pyrosequencing of short PCR products. A 48/45-bp stretch including primers of the amelogenin gene with a 3-bp insertion on the Y chromosome was chosen for analysis. In an initial study, we correctly typed 50 male and 50 female DNA samples from unrelated donors. First experiments with forensic samples, which failed in conventional analyses, indicate that this approach might be an advantage when dealing with degraded DNA.

  11. Structural diversity in serine derived homochiral metal organic frameworks

    Indian Academy of Sciences (India)

    Tanay Kundu; Rahul Banerjee

    2014-09-01

    Two new Zn(II) and Cd(II) based homochiral metal-organic frameworks (MOFs) [SerCdOAc and Zn(Ser)2] have been synthesized using pyridyl functionalized amino acid, viz., serine, as an organic linker. The SerCdOAc structure is three dimensional, while that of the Zn(Ser)2 is two dimensional. The polar voids of the corresponding MOFs are filled with solvent molecules (water in the case of SerCdOAc and methanol in the case of Zn(Ser)2). In both cases, metal centres, i.e., Zn(II) and Cd(II), are hexacoordinated. However, with a change in the solvent for synthesis, ligand coordinationmode and incorporation of additional coordinated anion resulted in a great change in the final MOF architecture. Herein, for the first time, we could achieve structural variety and synthesize MOFs composed of only metal ion and pyridyl functionalized amino acid linker.

  12. Liquid Metal-Organic Frameworks: Formation Mechanism, Structure and Properties

    OpenAIRE

    Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A.; Chapman, Karena W.; Keen, David A.; Bennett, Thomas D.; Coudert, François-Xavier

    2017-01-01

    Metal--organic frameworks are a novel family of chemically diverse materials, with applications in a wide field covering engineering, physics, chemistry, biology and medicine. Research so far has focused almost entirely on crystalline structures, yet a clear trend has emerged shifting the emphasis onto disordered states of MOFs, including "defective by design" crystals, as well as amorphous phases such as glasses and gels. Here we introduce a MOF liquid, a strongly associated liquid obtained ...

  13. Quantitative analysis of cellular metabolic dissipative, self-organized structures

    OpenAIRE

    Ildefonso Martínez de la Fuente

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the ...

  14. Additive Manufacturing of Biomedical Constructs with Biomimetic Structural Organizations

    Directory of Open Access Journals (Sweden)

    Xiao Li

    2016-11-01

    Full Text Available 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.

  15. 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.

  16. Organic and inorganic–organic thin film structures by molecular layer deposition: A review

    Directory of Open Access Journals (Sweden)

    Pia Sundberg

    2014-07-01

    Full Text Available The possibility to deposit purely organic and hybrid inorganic–organic materials in a way parallel to the state-of-the-art gas-phase deposition method of inorganic thin films, i.e., atomic layer deposition (ALD, is currently experiencing a strongly growing interest. Like ALD in case of the inorganics, the emerging molecular layer deposition (MLD technique for organic constituents can be employed to fabricate high-quality thin films and coatings with thickness and composition control on the molecular scale, even on complex three-dimensional structures. Moreover, by combining the two techniques, ALD and MLD, fundamentally new types of inorganic–organic hybrid materials can be produced. In this review article, we first describe the basic concepts regarding the MLD and ALD/MLD processes, followed by a comprehensive review of the various precursors and precursor pairs so far employed in these processes. Finally, we discuss the first proof-of-concept experiments in which the newly developed MLD and ALD/MLD processes are exploited to fabricate novel multilayer and nanostructure architectures by combining different inorganic, organic and hybrid material layers into on-demand designed mixtures, superlattices and nanolaminates, and employing new innovative nanotemplates or post-deposition treatments to, e.g., selectively decompose parts of the structure. Such layer-engineered and/or nanostructured hybrid materials with exciting combinations of functional properties hold great promise for high-end technological applications.

  17. Controlled Encapsulation of Functional Organic Molecules within Metal-Organic Frameworks: In Situ Crystalline Structure Transformation.

    Science.gov (United States)

    Guan, Jinju; Hu, Yu; Wang, Yu; Li, Hongfeng; Xu, Zhiling; Zhang, Tao; Wu, Peng; Zhang, Suoying; Xiao, Gengwu; Ji, Wenlan; Li, Linjie; Zhang, Meixuan; Fan, Yun; Li, Lin; Zheng, Bing; Zhang, Weina; Huang, Wei; Huo, Fengwei

    2017-03-01

    Functional organic molecules/metal-organic frameworks composites can be obtained by in situ crystalline structure transformation from ZIF-L to ZIF-8-L under double solvent conditions. Interestingly, the as-prepared molecules/ZIF-8-L composites with the leaf-like morphology exhibit good fluorescence properties and size selectivity in fluorescent quenchers due to the molecular sieving effect of the well-defined microporous ZIF-8-L. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Long-term organic fertilization effect on chernozem structure

    Science.gov (United States)

    Słowińska-Jurkiewicz, A.; Bryk, M.; Medvedev, V. V.

    2013-01-01

    The objective of the study was to examine the structure of typical Ukrainian chernozem developed on loess, which (I) had been fertilized by standard crop rotation since 1912 with farm yard manure at the rate of 16 t ha-1 and (II) had not been fertilized with farm yard manure by sugar beet monoculture since 1929. After harvest of winter wheat and sugar beet, the samples of undisturbed structure were taken from 5 layers of both profiles: 0-8, 10-18, 20-28, 30-38, and 40-48 cm. The morphological analysis of the structure of the investigated chernozem revealed that the most visible differences between the soil structures of the two pedons occurred in their superficial layers. The 0-18 cm layer of the soil in the experiment I had an aggregate structure, whereas analogous layer of the soil in experiment II was much more compacted. Below about 30 cm from the ground level both pedons had very similar structure. For the soil in the experiment I an appropriate crop rotation and regular supplies of organic matter allowed for preservation of a favourable structure even in the upper layers - in contrast to the soil in the experiment II.

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

    Science.gov (United States)

    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…

  20. Application of organic geochemistry to detect signatures of organic matter in the Haughton impact structure

    Science.gov (United States)

    Parnell, John; Lee, Pascal; Osinski, Gordon R.; Cockell, Charles S.

    2005-12-01

    Organic geochemistry applied to samples of bedrock and surface sediment from the Haughton impact structure detects a range of signatures representing the impact event and the transfer of organic matter from the crater bedrock to its erosion products. The bedrock dolomite contains hydrocarbon-bearing fluid inclusions which were incorporated before the impact event. Comparison of biomarker data from the hydrocarbons in samples inside and outside of the crater show the thermal signature of an impact. The occurrence of hydrocarbon inclusions in hydrothermal mineral samples shows that organic matter was mobilized and migrated in the immediate aftermath of the impact. The hydrocarbon signature was then transferred from bedrock to the crater-fill lacustrine deposits and present-day sediments in the crater, including wind-blown detritus in snow/ice. Separate signatures are detected from modern microbial life in crater rock and sediment samples. Signatures in Haughton crater samples are readily detectable because they include hydrocarbons generated by the burial of organic matter. This type of organic matter is not expected in crater samples on other planets, but the Haughton data show that, using very high resolution detection of organic compounds, any signature of primitive life in the crater rocks could be transferred to surface detritus and so extend the sampling medium.

  1. 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

  2. [Expression of thermostable recombiant Luciola lateralis luciferase and development of heat-stable pyrosequencing system].

    Science.gov (United States)

    Xu, Shu; Zou, Bingjie; Wang, Jianping; Wu, Haiping; Zhou, Guohua

    2012-06-01

    Pyrosequencing is a tool based on bioluminescence reaction for real-time analyzing DNA sequences. The sensitivity of pyrosequencing mainly depends on luciferase in reaction mixture. However, the instability of pyrosequencing reagents caused by fragile wild Photinus pyralis luciferase (PpL) in conventional pyrosequencing usually leads to unsatisfied results, which limits the application of pyrosequencing. In order to improve the stability of pyrosequencing reagents, the coding sequences of mutant thermostable Luciola lateralis luciferase (rt-LlL) was synthesized, and inserted into the plasmid of pET28a(+) to express the thermostable rt-LlL with a 6 x His-tag in the N terminal. The purified rt-LlL with the molecular mass of 60 kDa was obtained by Ni-affinity chromatography. The specific activity of rt-LlL was determined as 4.29 x 10(10) RLU/mg. Moreover, the thermostability of rt-LlL was investigated, and the results showed that rt-LlL had activity at 50 degrees C, and remained 90% of activity after incubated at 40 degrees C for 25 min. Finally, rt-LlL was used to substitute commercial Photinus pyralis luciferase in conventional pyrosequencing reagent to get thermostable pyrosequencing reagent. Comparing with conventional pyrosequencing reagent, the thermostable pyrosequencing reagent is more stable, and it's activity would not lose when incubated at 37 degrees C for 1 h. This study laid foundation of establishing reliable and stable pyrosequencing system which would be applied in Point-of-Care Testing.

  3. Necessity of Microdissecting Different Tumor Components in Pulmonary Tumor Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Dahui Qin

    2016-01-01

    Full Text Available Microdissection is a useful method in tissue sampling prior to molecular testing. Tumor heterogeneity imposes new challenges for tissue sampling. Different microdissecting methods have been employed in face of such challenge. We improved our microdissection method by separately microdissecting the morphologically different tumor components. This improvement helped the pyrosequencing data analysis of two specimens. One specimen consisted of both adenocarcinoma and neuroendocrine components. When both tumor components were sequenced together for KRAS (Kirsten rat sarcoma viral oncogene homolog gene mutations, the resulting pyrogram indicated that it was not a wild type, suggesting that it contained KRAS mutation. However, the pyrogram did not match any KRAS mutations and a conclusion could not be reached. After microdissecting and testing the adenocarcinoma and neuroendocrine components separately, it was found that the adenocarcinoma was positive for KRAS G12C mutation and the neuroendocrine component was positive for KRAS G12D mutation. The second specimen consisted of two morphologically different tumor nodules. When microdissected and sequenced separately, one nodule was positive for BRAF (v-raf murine sarcoma viral oncogene homolog B1 V600E and the other nodule was wild type at the BRAF codon 600. These examples demonstrate that it is necessary to microdissect morphologically different tumor components for pyrosequencing.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Tongjit Thanchomnang

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

  6. Organic synthetic environmental endocrine disruptors: structural classes and metabolic fate.

    Science.gov (United States)

    Schmidt, Jan; Peterlin-Mašič, Lucija

    2012-12-01

    Endocrine disruption is the modification of the endocrine system causing harmful effects in healthy subjects or their offspring. Physiological endocrine hormones act at very low plasma concentrations, and certain chemicals known as endocrine disrupting compounds (EDCs) are suspected of modifying endocrine function at similarly low concentrations. In our review we focus mainly on the structural classes of organic synthetic environmental endocrine disruptors and their common structural elements that enable them to interact with estrogen signalling. EDCs can affect estrogenic signalling directly through interaction with estrogen receptors (ERs) or indirectly through transcription factors such as the aryl hydrocarbon receptor (AhR) or by modulation of critical metabolic enzymes engaged in estrogen biosynthesis and metabolism. However, some structural elements can also pose a great risk of cytotoxicity and genotoxicity, especially after biotransformation to reactive metabolites.

  7. Polymorphic Microsatellite Loci for Virola sebifera (Myristicaceae Derived from Shotgun 454 Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Na Wei

    2013-04-01

    Full Text Available Premise of the study: Polymorphic microsatellite loci were characterized in the dioecious neotropical rainforest tree Virola sebifera. The markers will be used to study ecological and genetic impacts of hunting and landscape change in this vertebrate-dispersed, insect-pollinated tree species. Methods and Results: Simple sequence repeat (SSR markers were screened from genomic libraries of South American V. sebifera obtained by shotgun 454 pyrosequencing. Primer pairs were tested on Panamanian samples (N = 42. Approximately 52% of the 61 tested SSR markers amplified, and 16% were polymorphic. Ten selected polymorphic SSR loci contained seven to 15 alleles per locus, and polymorphic information content averaged 0.694. Observed heterozygosity ranged from 0.465 to 0.905, and expected heterozygosity was between 0.477 and 0.876. Conclusions: The 10 polymorphic loci will be useful in studying gene flow and genetic structure at local and regional spatial scales in V. sebifera.

  8. Organic matter and soil structure in the Everglades Agricultural Area

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Alan L. [Univ. of Florida, Gainesville, FL (United States); Hanlon, Edward A. [Univ. of Florida, Gainesville, FL (United States)

    2013-01-01

    This publication pertains to management of organic soils (Histosols) in the Everglades Agricultural Area (EAA). These former wetland soils are a major resource for efficient agricultural production and are important globally for their high organic matter content. Recognition of global warming has led to considerable interest in soils as a repository for carbon. Soils rich in organic matter essentially sequester or retain carbon in the profile and can contribute directly to keeping that sequestered carbon from entering the atmosphere. Identification and utilization of management practices that minimize the loss of carbon from organic soils to the atmosphere can minimize effects on global warming and increase the longevity of subsiding Histosols for agricultural use. Understanding and predicting how these muck soils will respond to current and changing land uses will help to manage soil carbon. The objectives of this document are to: a. Discuss organic soil oxidation relative to storing or releasing carbon and nitrogen b. Evaluate effects of cultivation (compare structure for sugarcane vs. uncultivated soil) Based upon the findings from the land-use comparison (sugarcane or uncultivated), organic carbon was higher with cultivation in the lower depths. There is considerable potential for minimum tillage and residue management to further enhance carbon sequestration in the sugarcane system. Carbon sequestration is improved and soil subsidence is slowed with sugarcane production, and both of these are positive outcomes. Taking action to increase or maintain carbon sequestration appears to be appropriate but may introduce some risk to farming operations. Additional management methods are needed to reduce this risk. For both the longevity of these organic soils and from a global perspective, slowing subsidence through BMP implementation makes sense. Since these BMPs also have considerable societal benefit, it remains to be seen if society will help to offset a part or all

  9. Abundance and diversity of bacteria in oxygen minimum drinking water reservoir sediments studied by quantitative PCR and pyrosequencing.

    Science.gov (United States)

    Zhang, Hai-han; Huang, Ting-lin; Chen, Sheng-nan; Yang, Xiao; Lv, Kai; Sekar, Raju

    2015-04-01

    Reservoir sediment is one of the most stressful environments for microorganisms due to periodically oxygen minimum conditions. In this study, the abundance and composition of bacteria associated with sediments from three drinking water reservoirs (Zhoucun, ZCR; Shibianyu, SBYR; and Jinpen, JPR) were investigated by quantitative polymerase chain reaction and 16S rRNA-based 454 pyrosequencing. The results of physico-chemical analysis of sediments showed that the organic matter and total nitrogen were significantly higher in ZCR as compared to JPR (P oxygen minimum and stressful freshwater environments.

  10. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway

    Directory of Open Access Journals (Sweden)

    Andrey M. Grishin

    2015-06-01

    Full Text Available Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.

  11. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway.

    Science.gov (United States)

    Grishin, Andrey M; Cygler, Miroslaw

    2015-06-12

    Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism-coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.

  12. 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.

  13. Comparison of DNA Pyrosequencing with Alternative Methods for Identification of Mycobacteria▿

    OpenAIRE

    2008-01-01

    Identification of mycobacterial clinical isolates by pyrosequencing within the hypervariable A region of the 16S rRNA gene was compared to other identification methods. For >90% of isolates, these identifications correlated to the level of complex or species. For identification of many mycobacteria, pyrosequencing offers an inexpensive alternative to traditional sequencing.

  14. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    Science.gov (United States)

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  15. Lanthanides caged by the organic chelates; structural properties.

    Science.gov (United States)

    Smentek, Lidia

    2011-04-13

    The structure, in particular symmetry, geometry and morphology of organic chelates coordinated with the lanthanide ions are analyzed in the present review. This is the first part of a complete presentation of a theoretical description of the properties of systems, which are widely used in technology, but most of all, in molecular biology and medicine. The discussion is focused on the symmetry and geometry of the cages, since these features play a dominant role in the spectroscopic activity of the lanthanides caged by organic chelates. At the same time, the spectroscopic properties require more formal presentation in the language of Racah algebra, and deserve a separate analysis. In addition to the parent systems of DOTA, DOTP, EDTMP and CDTMP presented here, their modifications by various antennas are analyzed. The conclusions that have a strong impact upon the theory of the energy transfer and the sensitized luminescence of these systems are based on the results of numerical density functional theory calculations.

  16. Study of organic solar cells with stacked bulk heterojunction structure

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin-fang; XU Zheng; ZHAO Su-ling; ZHANG Fu-jun; LI Yan; WU Chun-yu; CHEN Yue-ning

    2008-01-01

    Organic solar cells with stacked bulk heterojunction(BHJ) are investigated based on conjugated polymer. By using the solution spin-coating method, Poly[2-methoxy, 5-(2'-ethyl-hexyloxy) -1,4-phenylene vinylene] (MEH-PPV) and ZnO nanoparticles (50 nm) are mixed as the optical sense layer. Ag is used as inter-layer to connect the upper BILl cell and the lower cell. The structures are ITO/PEDOT:PSS/MEH-PPV/Ag/MEH-PPV:ZnO/Al. The open circuit voltage (Voc) of a stacked cell is about 3.7 times of that of an individual organic solar cell (ITO/PEDOT:PSS/MEH-PPV/A1). The short circuit current (Jsc) of a stacked cell is increased by about 1.6 times of that of individual one.

  17. Single-Walled Carbon-Nanotubes-Based Organic Memory Structures

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2017-08-01

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

  19. 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

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

    Directory of Open Access Journals (Sweden)

    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

  1. Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies.

    Science.gov (United States)

    Francioli, Davide; Schulz, Elke; Lentendu, Guillaume; Wubet, Tesfaye; Buscot, François; Reitz, Thomas

    2016-01-01

    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 parameters

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Christian Lohse

    2014-10-01

    Full Text Available 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.

  4. Molecular structure and exciton dynamics in organic conjugated polymers

    Science.gov (United States)

    Thomas, Alan K.

    Intermolecular electronic interactions, dipole coupling and orbital overlap, caused by pi-pi stacking in organic conjugated polymers lead to unique structures and properties that can be harnessed for optoelectronic applications. These interactions define structure-function relationships in amorphous and aggregated forms of polymers in the solid state and determine their efficiencies and functionality in electronic devices, from transistors to solar cells. Organic polymer electronic device performance depends critically upon electronic coupling between monomer units -mediated by conformation and packing characteristics - that dictates electronic properties like conductivity and capacitance as well as electronic processes, such as charge carrier generation and transport. This dissertation demonstrates how electronic processes in conjugated polymers are mediated by subtle inter- and intra-chain electronic interactions imparted by the conformational degrees of freedom within their solid state structure and how this effects device performance. To initiate this investigation into structure-function relationships, an examination of nanoparticles representing two limiting aggregation states of the conjugated polymer poly(3-hexylthiophene) (P3HT) was conducted. These aggregates are defined by their predominate form of electronic coupling, inter- or intrachain, called H- and J-aggregates respectively. H- or J-aggregates of P3HT were embedded in an insulating matrix and time-resolved fluorescence intensity modulation spectroscopy was utilized to uncover the existence of efficient singlet-triplet quenching in J aggregates not present in H-aggregates. These studies were extended by examining P3HT H-and J-aggregates under applied electric fields in capacitor type devices using multiple time-resolved and steady-state spectroscopic techniques. These experiments reveal electronic couplings in J aggregates that shift excited state population towards a majority composed of long lived

  5. Single-Crystal Structure of a Covalent Organic Framework

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  6. Similarities Between Biological and Social Networks in Their Structural Organization

    Science.gov (United States)

    Kahng, Byungnam; Lee, Deokjae; Kim, Pureun

    A branching tree is a tree that is generated through a multiplicative branching process starting from a root. A critical branching tree is a branching tree in which the mean branching number of each node is 1, so that the number of offspring neither decays to zero nor flourishes as the branching process goes on. Moreover, a scale-free branching tree is a branching tree in which the number of offspring is heterogeneous, and its distribution follows a power law. Here we examine three structures, two from biology (a phylogenetic tree and the skeletons of a yeast protein interaction network) and one from social science (a coauthorship network), and find that all these structures are scale-free critical branching trees. This suggests that evolutionary processes in such systems take place in bursts and in a self-organized manner.

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

    Directory of Open Access Journals (Sweden)

    Ingmar S Middelbos

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

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

    Science.gov (United States)

    Moya, Patricia; Molins, Arántzazu; Martínez-Alberola, Fernando; Muggia, Lucia; Barreno, Eva

    2017-01-01

    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 ecophysiological and

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    El-Sayed Yasser Y

    2007-11-01

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

  11. Structure and dynamics in self-organized C60 fullerenes.

    Science.gov (United States)

    Patnaik, Archita

    2007-01-01

    This manuscript on 'structure and dynamics in self-organized C60 fullerenes' has three sections dealing with: (A) pristine C60 aggregate structure and geometry in solvents of varying dielectric constant. Here, using positronium (Ps) as a fundamental probe which maps changes in the local electron density of the microenvironment, the onset concentration for stable C60 aggregate formation and its phase behavior is deduced from the specific interactions of the Ps atom with the surrounding. (B) A novel methanofullerene dyad, based on a hydrophobic (acceptor C60 moiety)-hydrophilic (bridge with benzene and ester functionalities)-hydrophobic (donor didodecyloxybenzene) network is chosen for investigation of characteristic self-assembly it undergoes leading to supramolecular aggregates. The pi-electronic amphiphile, necessitating a critical dielectric constant epsilon > or = 30 in binary THF-water mixtures, dictated the formation of bilayer vesicles as precursors for spherical fractal aggregates upon complete dyad extraction into a more polar water phase. (C) While the molecular orientation is dependent on the packing density, the ordering of the molecular arrangement, indispensable for self-assembly depends on the balance between the structures demanded by inter-molecular and molecule-substrate interactions. The molecular orientation in a monolayer affects the orientation in a multilayer, formed on the monolayer, suggesting the possibility of the latter to act as a template for controlling the structure of the three dimensionally grown self-assembled molecular aggregation. A systematic study on the electronic structure and orientation associated with C60 functionalized aminothiol self-assembled monolayers on Au(111) surface is presented using surface sensitive Ultra-Violet Photoelectron Spectroscopy (UPS) and C-K edge Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. The results revealed drastic modifications to d-band structure of Au(111) and the

  12. Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology.

    Science.gov (United States)

    Cardinali-Rezende, Juliana; Rojas-Ojeda, Patricia; Nascimento, Andréa M A; Sanz, José L

    2016-03-01

    Biomethanization entails a good means to reduce the organic fraction (OF) derived from municipal solid wastes (MSW). The bacterial diversity of a full scale MSW anaerobic reactor located in Madrid (Spain) was investigated using high-throughput 454 pyrosequencing. Even though the proteolytic bacteria prevailed throughout all of the process, community shifts were observed from the start-up to the steady-state conditions, with an increasing biodiversity displayed over time. The Bacteroidetes and the Firmicutes were the majority phyla: 55.1 and 40.2% (start-up) and 18.7 and 78.7 (steady-state) of the total reads. The system's lack of evenness remains noteworthy as the sequences affiliated to the proteolytic non-saccharolytic Proteiniphylum, Gallicola and Fastidiosipila genera, together with the saccharolytic Saccharofermentans, were predominant on the system and this predominance appears to correlate with the presence of a high ammonium concentration. The 454 pyrosequencing revealed a great diversity of rare organisms which seemingly do not sustain any metabolic roles in the course of the OF-MSW degradation. However, this scarce and unique microbiota can confer great resilience to the system as a buffer against nutritional and environmental changing conditions, thus opening the door to increase the current knowledge about the bacterial community dynamics taking place during MSW treatment processes.

  13. ORGANIZING SCENARIO VARIABLES BY APPLYING THE INTERPRETATIVE STRUCTURAL MODELING (ISM

    Directory of Open Access Journals (Sweden)

    Daniel Estima de Carvalho

    2009-10-01

    Full Text Available The scenario building method is a thought mode - taken to effect in an optimized, strategic manner - based on trends and uncertain events, concerning a large variety of potential results that may impact the future of an organization.In this study, the objective is to contribute towards a possible improvement in Godet and Schoemaker´s scenario preparation methods, by employing the Interpretative Structural Modeling (ISM as a tool for the analysis of variables.Given this is an exploratory theme, bibliographical research with tool definition and analysis, examples extraction from literature and a comparison exercise of referred methods, were undertaken.It was verified that ISM may substitute or complement the original tools for the analysis of variables of scenarios per Godet and Schoemaker’s methods, given the fact that it enables an in-depth analysis of relations between variables in a shorter period of time, facilitating both structuring and construction of possible scenarios.Key-words: Strategy. Future studies. Interpretative Structural Modeling.

  14. Social Capital in Organizations - Beyond Structure and Metaphor

    DEFF Research Database (Denmark)

    Waldstrøm, Christian

    2003-01-01

    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....... Secondly, it is necessary to determine whether social capital can or should be measured. Thirdly, the negative aspects of social capital should be explored and integrated into the existing research. Fourthly, the field between social capital of the individual and organizational social capital lacks...

  15. Nanoscale Structure of Organic Matter Could Explain Litter Decomposition

    Science.gov (United States)

    Papa, G.; Adani, F.

    2014-12-01

    According to the literature biochemical catalyses are limited in their actions because of the complex macroscopic and, above all, microscopic structures of cell wall that limit mass transportation (i.e. 3D structure). Our study on energy crop showed that plant digestibility increased by modifying the 3D cell wall microstructure. Results obtained were ascribed to the enlargement, such as effectively measured, of the pore spaces between cellulose fibrils. Therefore we postulated that 3 D structure of plant residues drives degradability in soil determining its recalcitrance in short time. Here we focused on the drivers of short-term decomposition of organic matter (plant residues) in soils evaluating the architecture of plant tissues, captured via measurements of the microporosiy of the cell walls. Decomposition rates of a wide variety of biomass types were studied conducting experiments in both aerobic and anaerobic environments. Different analytical approaches were applied in order to characterize biomass at both chemical and physical level. Combined statistical approaches were used to examine the relationships between carbon mineralization and chemical/physical characteristics. The results revealed that degradation was significantly and negatively correlated with the micro-porosity surface (MiS) (surface of pores of 0.3-1.5 nm of diameter). The multiple regressions performed by using partial least square model enabled describing biomass biodegradability under either aerobic and anaerobic condition by using micro-porosity and aromatic-C content (assumed to be representative of lignin) as independent variables (R2 =0.97, R2cv =0.95 for aerobic condition; R2 =0.99, R2cv =0.98 for anaerobic condition, respectively). These results corroborate the hypothesis that plant tissues are physically protected from enzymatic attack by a microporous "sheath" that limit penetration into cell wall, and demonstrate the key role played by aromatic carbon, because of its chemical

  16. Structural versatility of Metal-organic frameworks: Synthesis and Characterization

    KAUST Repository

    Alsadun, Norah S.

    2017-05-01

    Metal-Organic Frameworks (MOFs), an emerging class of porous crystalline materials, have shown promising properties for diverse applications such as catalysis, gas storage and separation. The high degree of tunability of MOFs vs other solid materials enable the assembly of advanced materials with fascinating properties for specific applications. Nevertheless, the precise control in the construction of MOFs at the molecular level remains challenging. Particularly, the formation of pre-targeted multi-nuclear Molecular Building Block (MBB) precursors to unveil materials with targeted structural characteristics is captivating. The aim of my master project in the continuous quest of the group of Prof. Eddaoudi in exploring different synthetic pathways to control the assembly of Rare Earth (RE) based MOF. After giving a general overview about MOFs, I will discuss in this thesis the results of my work on the use of tri-topic oriented organic carboxylate building units with the aim to explore the assembly/construction of new porous RE based MOFs. In chapter 2 will discuss the assembly of 3-c linkers with RE metals was then evaluated based on symmetry and angularity of the three connected linkers. The focus of chapter 3 is cerium based MOFs and heterometallic system, based on 3-c ligands with different length and symmetry. Overall, the incompatibility of 3-c ligands with the 12-c cuo MBB did not allow to any formation of higher neuclearity (˃6), but it has resulted in affecting the connectivity of the cluster.

  17. 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.

  18. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    Science.gov (United States)

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. © 2013 John Wiley & Sons Ltd.

  19. Structural spectral response tuning in organic deep ultraviolet photodetectors

    Science.gov (United States)

    Zhu, Lu; Wang, Wen-Shuo; Yao, Zhi-Gang; Zhang, Xi-Qing; Wang, Yong-Sheng

    2013-02-01

    We demonstrated novel organic deep ultraviolet photodetectors with structural spectral response tuning through bulk heterojunctions (HJs) and mixed planar-bulk HJs (PBHJs), respectively. TAPC and BAlq were utilized as the electron donor and acceptor, as well as polymer PEDOT:PSS was present as the transparent anode. The mixed PBHJs and bulk HJs reveal extremely low dark current of 3.35 × 10-8 and 2.94 × 10-8 A/cm2, and high photocurrent of 3.01 × 10-5 and 9.55 × 10-5 A/cm2 at -10 V under 260 nm light illumination with an intensity of 0.91 mW/cm2, respectively. A peak response of 33.6 mA/W at ˜260 nm and a detectivity of 3.24 × 1011 cm Hz1/2 W-1 are achieved in the mixed PBHJs. The bulk HJs exhibit a maximum response of 100.8 mA/W at ˜280 nm and a detectivity of 1.04 × 1012 cm Hz1/2 W-1. The photophysics involved in structural spectral response tuning are also discussed in detail.

  20. Adaptive symbiotic organisms search (SOS algorithm for structural design optimization

    Directory of Open Access Journals (Sweden)

    Ghanshyam G. Tejani

    2016-07-01

    Full Text Available The symbiotic organisms search (SOS algorithm is an effective metaheuristic developed in 2014, which mimics the symbiotic relationship among the living beings, such as mutualism, commensalism, and parasitism, to survive in the ecosystem. In this study, three modified versions of the SOS algorithm are proposed by introducing adaptive benefit factors in the basic SOS algorithm to improve its efficiency. The basic SOS algorithm only considers benefit factors, whereas the proposed variants of the SOS algorithm, consider effective combinations of adaptive benefit factors and benefit factors to study their competence to lay down a good balance between exploration and exploitation of the search space. The proposed algorithms are tested to suit its applications to the engineering structures subjected to dynamic excitation, which may lead to undesirable vibrations. Structure optimization problems become more challenging if the shape and size variables are taken into account along with the frequency. To check the feasibility and effectiveness of the proposed algorithms, six different planar and space trusses are subjected to experimental analysis. The results obtained using the proposed methods are compared with those obtained using other optimization methods well established in the literature. The results reveal that the adaptive SOS algorithm is more reliable and efficient than the basic SOS algorithm and other state-of-the-art algorithms.

  1. Modeling adsorption properties of structurally deformed metal-organic frameworks using structure-property map.

    Science.gov (United States)

    Jeong, WooSeok; Lim, Dae-Woon; Kim, Sungjune; Harale, Aadesh; Yoon, Minyoung; Suh, Myunghyun Paik; Kim, Jihan

    2017-07-25

    Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure-property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure-property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure-property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure-property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

  2. Orthographic structure versus morphological structure: principles of lexical organization in a given language.

    Science.gov (United States)

    Frost, Ram; Kugler, Tamar; Deutsch, Avital; Forster, Kenneth I

    2005-11-01

    Most models of visual word recognition in alphabetic orthographies assume that words are lexically organized according to orthographic similarity. Support for this is provided by form-priming experiments that demonstrate robust facilitation when primes and targets share similar sequences of letters. The authors examined form-orthographic priming effects in Hebrew, Arabic, and English. Hebrew and Arabic have an alphabetic writing system but a Semitic morphological structure. Hebrew morphemic units are composed of noncontiguous phonemic (and letter) sequences in a given word. Results demonstrate that form-priming effects in Hebrew or Arabic are unreliable, whereas morphological priming effects with minimal letter overlap are robust. Hebrew bilingual subjects, by contrast, showed robust form-priming effects with English material, suggesting that Semitic words are lexically organized by morphological rather than orthographic principles. The authors conclude that morphology can constrain lexical organization even in alphabetic orthographies and that visual processing of words is first determined by morphological characteristics.

  3. Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing

    Directory of Open Access Journals (Sweden)

    Herrera-Estrella Luis

    2009-07-01

    Full Text Available Abstract Background In-depth sequencing analysis has not been able to determine the overall complexity of transcriptional activity of a plant organ or tissue sample. In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs, although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure for validating gene prediction and estimating overall gene coverage. This approach could be very valuable for complex plant genomes. In addition, little emphasis has been given to efforts aiming at an estimation of the overall transcriptional universe found in a multicellular organism at a specific developmental stage. Results To explore, in depth, the transcriptional diversity in an ancient maize landrace, we developed a protocol to optimize the sequencing of cDNAs and performed 4 consecutive GS20–454 pyrosequencing runs of a cDNA library obtained from 2 week-old Palomero Toluqueño maize plants. The protocol reported here allowed obtaining over 90% of informative sequences. These GS20–454 runs generated over 1.5 Million reads, representing the largest amount of sequences reported from a single plant cDNA library. A collection of 367,391 quality-filtered reads (30.09 Mb from a single run was sufficient to identify transcripts corresponding to 34% of public maize ESTs databases; total sequences generated after 4 filtered runs increased this coverage to 50%. Comparisons of all 1.5 Million reads to the Maize Assembled Genomic Islands (MAGIs provided evidence for the transcriptional activity of 11% of MAGIs. We estimate that 5.67% (86,069 sequences do not align with public ESTs or annotated genes, potentially representing new maize transcripts. Following the assembly of 74.4% of the reads in 65,493 contigs, real-time PCR of selected genes confirmed a predicted correlation between the abundance of GS20–454 sequences and corresponding levels of gene expression. Conclusion A protocol was developed that significantly

  4. Structural organization of the inactive X chromosome in the mouse.

    Science.gov (United States)

    Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job

    2016-07-28

    X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions,remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes indifferent neural progenitor clones are associated with the presence of different TAD

  5. Inferring viral quasispecies spectra from 454 pyrosequencing reads

    Directory of Open Access Journals (Sweden)

    Măndoiu Ion

    2011-07-01

    Full Text Available Abstract Background RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences. Results In this paper, we introduce a new Viral Spectrum Assembler (ViSpA method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons, and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at http

  6. Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus and Chromera velia on the Great Barrier Reef, Australia.

    Directory of Open Access Journals (Sweden)

    Jan Slapeta

    Full Text Available BACKGROUND: The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. "type-N" symbiont belonging to the obligatory parasitic phylum Apicomplexa (Alveolata is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. METHODS & PRINCIPAL FINDINGS: We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus. We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. SIGNIFICANCE: This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef

  7. Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan “type-N” (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia

    Science.gov (United States)

    Šlapeta, Jan; Linares, Marjorie C.

    2013-01-01

    Background The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. “type-N” symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. Methods & Principal Findings We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa - Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. Significance This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is

  8. Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia.

    Science.gov (United States)

    Slapeta, Jan; Linares, Marjorie C

    2013-01-01

    The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. "type-N" symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these

  9. 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.

  10. Utilizing Pyrosequencing and Quantitative pCR to Characterize Fungal Populations among House Dust Samples

    Science.gov (United States)

    Molecular techniques are an alternative to culturing and counting methods in quantifying indoor fungal contamination. Pyrosequencing offers the possibility of identifying unexpected indoor fungi. In this study, 50 house dust samples were collected from homes in the Yakima Valley,...

  11. Pyrosequencing Analysis of Bench-Scale Nitrifying BiofiltersRemoving Trihalomethanes

    Science.gov (United States)

    The bacterial biofilm communities in four nitrifying biofilters degrading regulated drinking water trihalomethanes were characterized by 454 pyrosequencing. The three most abundant phylotypes based on total diversity were Nitrosomonas (70%), Nitrobacter (14%), and Chitinophagace...

  12. DNA Methylation Pyrosequencing Assay Is Applicable for the Assessment of Epigenetic Active Environmental or Clinical Relevant Chemicals

    Directory of Open Access Journals (Sweden)

    Ana-Maria Florea

    2013-01-01

    Full Text Available Exposure of cells and organisms to stressors might result in epigenetic changes. Here it is shown that investigation of DNA methylation using pyrosequencing is an alternative for in vitro and in vivo toxicological testing of epigenetic effects induced by chemicals and drugs. An in vitro evaluation of global and CpG site specific DNA methylation upon treatment of cells with chemicals/drugs is shown. Bisulfite genomic sequencing of methylation controls showed high methylation of LINE1 in methylation positive control and low methylation in the negative controls. The CpG sites within the LINE1 element are methylated at different levels. In vitro cell cultures show a methylation level ranging from 56% to 49%. Cultures of drug resistant tumor cells show significant hypomethylation as compared with the originating nonresistant tumor cells. The in vitro testing of epigenetically active chemicals (5-methyl-2’-deoxycytidine and trichostatin A revealed a significant change of LINE1 methylation status upon treatment, while specific CpG sites were more prone to demethylation than others (focal methylation. In conclusion, DNA methylation using pyrosequencing might be used not only for testing epigenetic toxins/drugs but also in risk assessment of drugs, food, and environmental relevant pollutants.

  13. 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.

  14. 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.

  15. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies.

    Science.gov (United States)

    Lüke, Claudia; Frenzel, Peter

    2011-09-01

    We analyzed the potential of pmoA amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic pmoA lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.

  16. Macrolide resistance determination and molecular typing of Mycoplasma pneumoniae by pyrosequencing.

    Science.gov (United States)

    Spuesens, Emiel B M; Hoogenboezem, Theo; Sluijter, Marcel; Hartwig, Nico G; van Rossum, Annemarie M C; Vink, Cornelis

    2010-09-01

    The first choice antibiotics for treatment of Mycoplasma pneumoniae infections are macrolides. Several recent studies, however, have indicated that the prevalence of macrolide (ML)-resistance, which is determined by mutations in the bacterial 23S rRNA, is increasing among M. pneumoniae isolates. Consequently, it is imperative that ML-resistance in M. pneumoniae is rapidly detected to allow appropriate and timely treatment of patients. We therefore set out to determine the utility of pyrosequencing as a convenient technique to assess ML-resistance. In addition, we studied whether pyrosequencing could be useful for molecular typing of M. pneumoniae isolates. To this end, a total of four separate pyrosequencing assays were developed. These assays were designed such as to determine a short genomic sequence from four different sites, i.e. two locations within the 23S rRNA gene, one within the MPN141 (or P1) gene and one within the MPN528a gene. While the 23S rRNA regions were employed to determine ML-resistance, the latter two were used for molecular typing. The pyrosequencing assays were performed on a collection of 108 M. pneumoniae isolates. The ML-resistant isolates within the collection (n=4) were readily identified by pyrosequencing. Moreover, each strain was correctly typed as either a subtype 1 or subtype 2 strain by both the MPN141 and MPN528a pyrosequencing test. Interestingly, two recent isolates from our collection, which were identified as subtype 2 strains by the pyrosequencing assays, were found to carry novel variants of the MPN141 gene, having rearrangements in each of the two repetitive elements (RepMP4 and RepMP2/3) within the gene. In conclusion, pyrosequencing is a convenient technique for ML-resistance determination as well as molecular typing of M. pneumoniae isolates.

  17. Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism.

    Science.gov (United States)

    Saliou, Adrien; Delobel, Pierre; Dubois, Martine; Nicot, Florence; Raymond, Stéphanie; Calvez, Vincent; Masquelier, Bernard; Izopet, Jacques

    2011-06-01

    There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays.

  18. Synthesis and structure determination of uranyl peroxide nanospheres in the presence of organic structure directing agents

    Science.gov (United States)

    Forbes, T. Z.; Burns, P. C.

    2007-12-01

    Recently, actinyl peroxide nanoclusters containing 20, 24, 28, or 32 actinyl polyhedra have been synthesized and their structures identified with single crystal X-ray diffraction [1]. Most nanomaterials are composed of main group elements or transition metals, therefore, these actinyl nanospheres may display vastly different chemical and physical properties due to the presence of filled f-orbitals. A major goal of our research group is to create novel actinyl materials, focusing on nano- and mesoporous materials. The original nanosphere syntheses were limited to inorganic crystallization agents, such as monovalent cations. Over the last decade, the use of organic compounds and surfactants have received increased attention as structure-directing agents for the generation of novel inorganic materials. Using structure-directing organic amines we have successfully synthesized and determined the structures of uranyl nanospheres containing 40 and 50 uranyl polyhedra. The topology of the skeletal U-50 nanosphere is identical to the C50Cl10 fullerene [2]. The topographical relationship between the actinyl nanospheres and fullerene or fullerene-like material may provide additional insight into stable configurations for lower fullerenes. [1] Burns et al., Actinyl peroxide nanospheres. Angewandte Chemie, International Edition, 2005. 44(14): p. 2135. [2] Xie et al., Capturing the Labile Fullerene[50] as C50Cl10. Science, (2004) 305(5671): p. 699.

  19. Resonance energy transfer in self-organized organic/inorganic dendrite structures

    Science.gov (United States)

    Melnikau, D.; Savateeva, D.; Lesnyak, V.; Gaponik, N.; Fernández, Y. Núnez; Vasilevskiy, M. I.; Costa, M. F.; Mochalov, K. E.; Oleinikov, V.; Rakovich, Y. P.

    2013-09-01

    Hybrid materials formed by semiconductor quantum dots and J-aggregates of cyanine dyes provide a unique combination of enhanced absorption in inorganic constituents with large oscillator strength and extremely narrow exciton bands of the organic component. The optical properties of dendrite structures with fractal dimension 1.7-1.8, formed from J-aggregates integrated with CdTe quantum dots (QDs), have been investigated by photoluminescence spectroscopy and fluorescence lifetime imaging microscopy. Our results demonstrate that (i) J-aggregates are coupled to QDs by Förster-type resonant energy transfer and (ii) there are energy fluxes from the periphery to the centre of the structure, where the QD density is higher than in the periphery of the dendrite. Such an anisotropic energy transport can be only observed when dendrites are formed from QDs integrated with J-aggregates. These QD/J-aggregate hybrid systems can have applications in light harvesting systems and optical sensors with extended absorption spectra.

  20. Multiplex PCR based on a universal biotinylated primer to generate templates for pyrosequencing.

    Science.gov (United States)

    Chen, Zhiyao; Liu, Yunlong; Duan, Wenbang; Ye, Hui; Wu, Haiping; Li, Jinheng; Zhou, Guohua

    2014-06-01

    Pyrosequencing is a powerful tool widely used in genetic analysis, however template preparation prior to pyrosequencing is still costly and time-consuming. To achieve an inexpensive and labor-saving template preparation for pyrosequencing, we have successfully developed a single-tube multiplex PCR including a pre-amplification and a universal amplification. In the process of pre-amplification, a low concentration of target-specific primers tagged with universal ends introduced universal priming regions into amplicons. In the process of universal amplification, a high concentration of universal primers was used for yielding amplicons with various SNPs of interest. As only a universal biotinylated primer and one step of single-stranded DNA preparation were required for typing multiple SNPs located on different sequences, pyrosequencing-based genotyping became time-saving, labor-saving, sample-saving, and cost-saving. By a simple optimization of multiplex PCR condition, only a 4-plex and a 3-plex PCR were required for typing 7 SNPs related to tamoxifen metabolism. Further study showed that pyrosequencing coupled with an improved multiplex PCR protocol allowed around 30% decrease of either typing cost or typing labor. Considering the biotinylated primer and the optimized condition of the multiplex PCR are independent of SNP locus, it is easy to use the same condition and the identical biotinylated primer for typing other SNPs. The preliminary typing results of the 7 SNPs in 11 samples demonstrated that multiplex PCR-based pyrosequencing could be promising in personalized medicine at a low cost.

  1. Marsh Soil Responses to Nutrients: Belowground Structural and Organic Properties.

    Science.gov (United States)

    Coastal marsh responses to nutrient enrichment apparently depend upon soil matrix and whether the system is primarily biogenic or minerogenic. Deteriorating organic rich marshes (Jamaica Bay, NY) receiving wastewater effluent had lower belowground biomass, organic matter, and soi...

  2. The Structural-functional Organization of the Urban Landschaft

    Directory of Open Access Journals (Sweden)

    Vasile GUŢULEAC

    2008-09-01

    Full Text Available The structure of the anthropic landschaft characterizes its internal organization, the connections between its components and the natural-anthropic associations of an inferior degree.The anthropic layer is to be analyzed in analogy with the natural component of the landschaft, which includes architectural edifices, communications, the geological component,the anthropic vegetation, the barren heaps resulted from mining activities, etc. The parametres of the anthropic components of the landschaft are the free surface, the built surface, the heightof the buildings and the density.The different geographical elements are reconstituted on the basis of NTCs (National Territorial Complex, separated on subtypes according to their specific (NTC IV – functionallandschaft area, NTC III – human settlement, NTC II – technogene fenced-in district, NTC I– technogene lot. We emphasized the features of these organizational types after we had donemuch research in field and in laboratory. We managed to draw a landschaft – functional mapof Czernowitz town, with a scale of 1: 10 000. We managed to detect 125 types of anthropiccomplex of lanschaft.For the urban territory we proposed two types of classification for the landschaftsystems: 1. NTCs that existed before the intense industrial anthropization; 2. technohenenatural complexes. The map of the anthropic-landschaft complexes of the town can be used asa basis for the geo-chemical map and for some applicative maps, especially ecological ones.

  3. Structural organization and interactions of transmembrane domains in tetraspanin proteins

    Directory of Open Access Journals (Sweden)

    DeGrado William F

    2005-06-01

    Full Text Available Abstract Background Proteins of the tetraspanin family contain four transmembrane domains (TM1-4 linked by two extracellular loops and a short intracellular loop, and have short intracellular N- and C-termini. While structure and function analysis of the larger extracellular loop has been performed, the organization and role of transmembrane domains have not been systematically assessed. Results Among 28 human tetraspanin proteins, the TM1-3 sequences display a distinct heptad repeat motif (abcdefgn. In TM1, position a is occupied by structurally conserved bulky residues and position d contains highly conserved Asn and Gly residues. In TM2, position a is occupied by conserved small residues (Gly/Ala/Thr, and position d has a conserved Gly and two bulky aliphatic residues. In TM3, three a positions of the heptad repeat are filled by two leucines and a glutamate/glutamine residue, and two d positions are occupied by either Phe/Tyr or Val/Ile/Leu residues. No heptad motif is apparent in TM4 sequences. Mutations of conserved glycines in human CD9 (Gly25 and Gly32 in TM1; Gly67 and Gly74 in TM2 caused aggregation of mutant proteins inside the cell. Modeling of the TM1-TM2 interface in CD9, using a novel algorithm, predicts tight packing of conserved bulky residues against conserved Gly residues along the two helices. The homodimeric interface of CD9 was mapped, by disulfide cross-linking of single-cysteine mutants, to the vicinity of residues Leu14 and Phe17 in TM1 (positions g and c and Gly77, Gly80 and Ala81 in TM2 (positions d, g and a, respectively. Mutations of a and d residues in both TM1 and TM2 (Gly25, Gly32, Gly67 and Gly74, involved in intramolecular TM1-TM2 interaction, also strongly diminished intermolecular interaction, as assessed by cross-linking of Cys80. Conclusion Our results suggest that tetraspanin intra- and intermolecular interactions are mediated by conserved residues in adjacent, but distinct regions of TM1 and TM2. A key

  4. Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques

    Directory of Open Access Journals (Sweden)

    Parham Peter

    2011-06-01

    Full Text Available Abstract Background Human killer immunoglobulin-like receptors (KIRs play a critical role in governing the immune response to neoplastic and infectious disease. Rhesus macaques serve as important animal models for many human diseases in which KIRs are implicated; however, the study of KIR activity in this model is hindered by incomplete characterization of KIR genetics. Results Here we present a characterization of KIR genetics in rhesus macaques (Macaca mulatta. We conducted a survey of KIRs in this species, identifying 47 novel full-length KIR sequences. Using this expanded sequence library to build upon previous work, we present evidence supporting the existence of 22 Mamu-KIR genes, providing a framework within which to describe macaque KIRs. We also developed a novel pyrosequencing-based technique for KIR genotyping. This method provides both comprehensive KIR genotype and frequency estimates of transcript level, with implications for the study of KIRs in all species. Conclusions The results of this study significantly improve our understanding of macaque KIR genetic organization and diversity, with implications for the study of many human diseases that use macaques as a model. The ability to obtain comprehensive KIR genotypes is of basic importance for the study of KIRs, and can easily be adapted to other species. Together these findings both advance the field of macaque KIRs and facilitate future research into the role of KIRs in human disease.

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

    Directory of Open Access Journals (Sweden)

    Lisa-Maree Gulino

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

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

    Directory of Open Access Journals (Sweden)

    Asker Noomi

    2009-07-01

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

  7. 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.

  8. Study on the local atomic structure of germanium in organic germanium compounds by EXAFS

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Organic germanium compounds have been extensively applied in medicine as tonics,In this paper,the local structures of two organic germanium compounds,carboxyethylgermanium sesquioxide and polymeric germanium glutamate,were determined by EXAFS.The structure parameters including coordination numbers and bond lengths were reported,and possible structure patterns were discussed.

  9. Organic modification of layered silicates. Structural and thermal characterizations

    Energy Technology Data Exchange (ETDEWEB)

    Prado, L.A.S. de A.; Schulte, K. [Polymer Composites, Denickstrasse 15, TU Hamburg-Harburg, D-21073 Hamburg (Germany); Karthikeyan, C.S.; Nunes, S.P. [Institute of Chemistry, GKSS Research Centre, Max-Planck Strasse 1, D-21502 Geesthacht (Germany); De Torriani, Iris L. [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, Cidade Universitaria Zeferino Vaz, CEP 13083-970, Campinas-SP (Brazil)

    2005-05-01

    Organic modification of natural and synthetic layered silicates namely montmorillonite and laponite is reported in this work. The modified silicates are being subsequently used in the preparation of nano-composite membranes based on ionomers for fuel cells application. Laponite, an entirely synthetic silicate, was modified using organosiloxanes containing imidazole groups. Two different strategies were adopted for modification: (a) swelling of the silicate in 2-butanone followed by functionalization using the siloxane at room temperature, (b) direct reaction between laponite and the organosiloxane in xylene at 120{sup o}C. Montmorillonite, a natural silicate, was supplied in the alkyl-ammonium form containing -OH groups. The modification of this silicate was conducted following the procedure (b). The structures of both plain and modified silicates were investigated by XRD showing that the interlayer distance (around 17A) was not affected during the functionalization of laponite. However, a noticeable increase in the interlayer distance from 18.0A to 24.5A was observed for the modified montmorillonite. This clearly shows the presence of polysiloxane chains in between the silicate layers. Further characterization showed that the modification of these silicates was in the range between 16% and 23% (molar percentage). TGA was done between 25 and 300{sup o}C in order to study the thermal degradation pattern of the silicates. The amount of adsorbed water could be determined from the results. The functionalization reduced the adsorption of water from 13.5% to 6.8% for laponite and from 8.5% to 4% for montmorillonite.

  10. Automatic Structure Determination of Organic Molecules: Principle and Implementation of the LSD Program

    Institute of Scientific and Technical Information of China (English)

    NUZILLARD,Jean-Marc

    2003-01-01

    The LSD (Logic for Structure Determination) program generates organic molecular structures from 1D and 2D NMR data without resorting to chemical shift databases. Its use in the resolution of natural product structure determination problems has been already reported in the literature. This paper describes how data and structures are internally represented and processed by LSD to build solution structures.

  11. 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...

  12. Organic solid solution composed of two structurally similar porphyrins for organic solar cells.

    Science.gov (United States)

    Zhen, Yonggang; Tanaka, Hideyuki; Harano, Koji; Okada, Satoshi; Matsuo, Yutaka; Nakamura, Eiichi

    2015-02-18

    A solid solution of a 75:25 mixture of tetrabenzoporphyrin (BP) and dichloroacenaphtho[q]tribenzo[b,g,l]porphyrin (CABP) forms when they are generated in a matrix of (dimethyl(o-anisyl)silylmethyl)(dimethylphenylsilylmethyl)[60]fullerene. This solid solution provides structural and optoelectronic properties entirely different from those of either pristine compounds or a mixture at other blending ratios. The use of this BP:CABP solid solution for organic solar cell (OSC) devices resulted in a power conversion efficiency (PCE) value higher by 16 and 300% than the PCE values obtained for the devices using the single donor BP and CABP, respectively, in a planar heterojunction architecture. This increase originates largely from the increase in short circuit current density, and hence by enhanced charge carrier separation at the donor/acceptor interface, which was probably caused by suitable energy level for the solid solution state, where electronic coupling between the two porphyrins occurred. The results suggest that physical and chemical modulation in solid solution is beneficial as an operationally simple method to enhance OSC performance.

  13. Fabrication and characterization of materials and structures for hybrid organic-inorganic photonics

    Science.gov (United States)

    Haško, Daniel; Chovan, Jozef; Uherek, František

    2017-03-01

    Hybrid organic-inorganic integrated photonics integrate the organic material, as a part of active layer, with inorganic structure, and it is the organic component that extends the functionalities as compared to inorganic photonics. This paper presents the results of fabrication and characterization of inorganic and organic layers, as well as of hybrid organic-inorganic structures. Inorganic oxide and nitride materials and structures were grown using plasma enhanced chemical vapor deposition. As a substrate for tested organic layers and for preparation of multilayer structures, commercially available SiO2 created by thermal oxidation on Si was used. The hybrid organic-inorganic structures were prepared by spin coating of organic materials on SiO2/Si inorganic structures. As the basic photonics devices, the testing strip inorganic and organic waveguides were fabricated using reactive ion etching. The shape of fabricated testing waveguides was trapezoidal and etched structures were able to guide the radiation. The presented technology enabled to prepare hybrid organic-inorganic structures of comparable dimensions and shape. The fabricated waveguides dimensions and shape will be used for optimisation and design of new lithographic mask to prepare photonic components with required characteristics.

  14. Perceptual Organization of Visual Structure Requires a Flexible Learning Mechanism

    Science.gov (United States)

    Aslin, Richard N.

    2011-01-01

    Bhatt and Quinn (2011) provide a compelling and comprehensive review of empirical evidence that supports the operation of principles of perceptual organization in young infants. They also have provided a comprehensive list of experiences that could serve to trigger the learning of at least some of these principles of perceptual organization, and…

  15. THE EXTENT OF CLONAL STRUCTURE IN DIFFERENT LYMPHOID ORGANS

    NARCIS (Netherlands)

    HERMANS, MHA; WUBBENA, A; KROESE, FGM; HUNT, SV; COWAN, R; OPSTELTEN, D

    1992-01-01

    To gain insight into the clonal organization of lymphoid organs, we studied the distribution in situ of donor-derived cells in near-physiological chimeras. We introduced RT7b fetal liver cells into nonirradiated congenic RT7a neonatal rats. The chimerism 6-20 wk after injection ranged from 0.3 to 20

  16. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  17. Microbial community in anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454 pyrosequencing analysis.

    Science.gov (United States)

    Ning, Xinqiang; Qiao, Wenwen; Zhang, Lei; Gao, Xu

    2014-12-01

    Modification of the anoxic-oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic-oxic-settling-anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased.

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

    Directory of Open Access Journals (Sweden)

    Juan M. Arroyo

    2013-12-01

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

  19. 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.

  20. 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.

  1. Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.

    Science.gov (United States)

    Onmus-Leone, Fatma; Hang, Jun; Clifford, Robert J; Yang, Yu; Riley, Matthew C; Kuschner, Robert A; Waterman, Paige E; Lesho, Emil P

    2013-01-01

    Despite major advances in next-generation sequencing, assembly of sequencing data, especially data from novel microorganisms or re-emerging pathogens, remains constrained by the lack of suitable reference sequences. De novo assembly is the best approach to achieve an accurate finished sequence, but multiple sequencing platforms or paired-end libraries are often required to achieve full genome coverage. In this study, we demonstrated a method to assemble complete bacterial genome sequences by integrating shotgun Roche 454 pyrosequencing with optical whole genome mapping (WGM). The whole genome restriction map (WGRM) was used as the reference to scaffold de novo assembled sequence contigs through a stepwise process. Large de novo contigs were placed in the correct order and orientation through alignment to the WGRM. De novo contigs that were not aligned to WGRM were merged into scaffolds using contig branching structure information. These extended scaffolds were then aligned to the WGRM to identify the overlaps to be eliminated and the gaps and mismatches to be resolved with unused contigs. The process was repeated until a sequence with full coverage and alignment with the whole genome map was achieved. Using this method we were able to achieved 100% WGRM coverage without a paired-end library. We assembled complete sequences for three distinct genetic components of a clinical isolate of Providencia stuartii: a bacterial chromosome, a novel bla NDM-1 plasmid, and a novel bacteriophage, without separately purifying them to homogeneity.

  2. 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.

  3. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

    Directory of Open Access Journals (Sweden)

    Chiusano Maria

    2009-08-01

    Full Text Available Abstract Background Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits. Results Fruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface. Conclusion Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

  4. 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.

  5. Giddens' "structuration," Luhmann's "self-organization," and the operationalization of the dynamics of meaning

    CERN Document Server

    Leydesdorff, Loet

    2009-01-01

    Luhmann's social systems theory and Giddens' structuration theory of action share an emphasis on reflexivity, but focus on meaning along a divide between inter-human communication and intentful action as two different systems of reference. Recombining these two theories, simulations of interaction, organization, and self-organization of intentional communication can be distinguished by using algorithms from the computation of anticipatory systems. The self-organizing and organizing layers remain rooted in the double contingency of the human encounter which provides the variation. Organization and self-organization of communication are reflexive upon and therefore reconstructive of each other. Using mutual information in three dimensions, the imprint of meaning processing in the modeling system on the historical organization of uncertainty in the modeled system can be measured. This is shown empirically in the case of intellectual organization as "structurating" structure in the textual domain of scientific ar...

  6. Pyrosequencing for detection of drug resistant relevant mutation in the polymerase gene of hepatitis B virus and its clinical application

    Institute of Scientific and Technical Information of China (English)

    陈占国

    2014-01-01

    Objective To explore the accuracy and clinical application of pyrosequencing for detection of drug resistant relevant mutation in the polymerase gene of hepatitis B virus(HBV).Methods Compared with Sanger sequencing,the accuracy and sensitivity of pyrosequencing were assessed.Pyrosequencing was used to determine the serum of 1 164 patients with chronic Hepatitis B and its re-sults were analyzed.Results The sensitivity of pyrosequencing was 1×103KIU/L,the same as Sanger sequencing.But

  7. Making a Self-feeding Structure by Assembly of Digital Organs

    Science.gov (United States)

    Cussat-Blanc, Sylvain; Luga, Hervé; Duthen, Yves

    In Nature, the intrinsic cooperation between organism's parts is capital. Most living systems are composed of organs, functional units specialized for specific actions. In our last research, we developed an evolutionary model able to generate artificial organs. This paper deals with the assembly of organs. We show, through experimentation, the development of an artificial organism composed of four digital organs able to produce a self-feeding organism. This kind of structure has applications in the mophogenetic-engineering of future nano and bio robots.

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

    Science.gov (United States)

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

    2016-03-01

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

  9. Psychodiagnosis of personality structure. II: Borderline personality organization.

    Science.gov (United States)

    Acklin, M W

    1993-10-01

    The borderline conditions have been the focus of considerable debate and controversy for over 30 years. This article, second in a series of three articles focusing on Kernberg's (1975, 1984) psychostructural diagnosis of personality organization, examines Rorschach contributions to the description and diagnosis of borderline personality organization. Rorschach approaches integrating nomothetic and idiographic data are applied to borderline personality functioning and appraised in light of the Rorschach's contribution to the clarification of the controversial and poorly delineated borderline diagnosis.

  10. Organic Farm Structure by Category of Agricultural Use

    Directory of Open Access Journals (Sweden)

    Manuela Dora Orboi

    2015-10-01

    Full Text Available Organic production systems are based on specific and precise standards of production, pursuing the achievement of optimal agro-systems, easy to sustain in terms of social, environmental and economic. Organic production systems plays a dual social role, because, on the one hand provides for a specific market that is responding to consumer demand for organic products, and on the other hand delivers public goods, contributing to environmental protection, animal welfare and rural development. The main goal of organic agriculture is to optimize the health and productivity of interdependent communities of soil, plants, animals and humans, providing new guidance of agricultural diversification in a general context of protecting the environment and promoting the development of sustainable agriculture. In 2013, the continent with the largest organic cultivated surface was Australia / Oceania, over 17.3 million, up to 5 million hectares compared to 2011, followed by Europe with 11.4 mil. Ha, Latin America - 6.6 million ha, Asia - 3.4 million ha North America - 3.0 million ha and Africa - 1.2 million ha of the 43.1 million total hectares grown in organic management system, almost two thirds are permanent pastures (27 million hectares, followed by agricultural land area totaling 10.9 million ha (arable land - 7.7 million ha permanent crops - 3.2 million ha.

  11. 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

    Directory of Open Access Journals (Sweden)

    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

  12. 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…

  13. 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.

  14. 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…

  15. 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;…

  16. Structural characteristics and development of ampullary organs in Acipenser naccarii.

    Science.gov (United States)

    Camacho, Susana; Ostos, Maria Del Valle; Llorente, José Ignacio; Sanz, Ana; García, Manuel; Domezain, Alberto; Carmona, Ramón

    2007-09-01

    Ampullary organs of Acipenser naccarii sturgeons were examined by optical and electronic microscopy (transmission electron microscopy and scanning electron microscopy) from hatching until 1 month later when the juvenile phase is completely established. It was observed that, when A. naccarii begins to feed actively, the ultrastructural characteristics of ampullary organs already correspond to those of adult animals. These organs may, therefore, be functional and, together with taste buds, facilitate food search after exhaustion of yolk sac food reserves. Mature ampullary organs of A. naccarii are formed by an ampulla that communicates with the exterior by means of a short channel. These ampullae correspond to the sensory portion of these receptors and are formed by two cell types: receptor cells and support cells. Receptor cells present a kinocilium on their free surface and establish ribbon synapses with axon nerve endings that arise from the underlying conjunctive tissue. Support cells enclose receptor cells, bear stereocilia and occasional cilia, and are of a secretory nature. The mucus associated with ampullary organs mainly comprises neutral mucopolysaccharides, whereas mucopolysaccharides are usually acid in other fish groups.

  17. Lewis acidic metal catalysed organic transformations by designed multi-component structures and assemblies

    Indian Academy of Sciences (India)

    Afsar Ali; Amit P Singh; Rajeev Gupta

    2010-05-01

    This paper presents the recent developments in designing multi-component structures including metal-organic frameworks containing Lewis acidic metal ions. The emphasis has been given to understand the design elements adopted to synthesize such structures bearing Lewis acidic metal ion. Further, few important Lewis acidic metal catalysed organic transformation reactions have been discussed demonstrating the importance of such materials for practical purposes.

  18. Design of control adaptability system model for TV media organization structure

    Institute of Scientific and Technical Information of China (English)

    WANG Dong-dong; WANG Ya-lin; MA Tao

    2008-01-01

    To resolve the control adaptability problem of TV media in complex competitive environment, a con-trol system model of TV media organization structure was designed. Based on the designed system model for TV media organization structure, the relations among the main factors of the system constitution, missions, organi-zing decision entity, and carrying bodies were analyzed. By means of applying multi-objective decision method and complex control system theory, and combining the integration model of TV media organization structure, the basic model was concluded and the corresponding parameters were designed. The current organization process of TV media is analyzed by this model, which comes to the adaptability appearance with different parameters. The results indicate that the model can estimate current TV media organization structure for the chain appearance of communications and the correlation between platforms and policy-making agencies.

  19. Studies on the Structure Evolvement of Organic Agricultural Industry in Taiwan and its Influential Factors

    Institute of Scientific and Technical Information of China (English)

    Xin; XU; Zheng; ZHANG; Li; KONG

    2014-01-01

    In order to study the development of organic agriculture in Taiwan in recent years,and based on relevant agriculture,economic and social statistics,the general scale of organic agriculture and industrial structure were treated with statistic analysis. Results suggest that the general scale of organic agriculture in Taiwan grew rapidly from 2004 to 2011. The certified organic farmers grew by 140. 59%,and the area with organic plantation grew by 302. 40%. The industrial structure has changed significantly as vegetables have become the No. 1 organic crop instead of rice. Besides of the four major crops,organic plantation has played an increasingly important role. Essential factors influencing the great-leap-forward development include the general trend of agricultural industrial structure adjustment,proliferation of management system and strategic opportunities brought by economic cycles.

  20. INMARSAT - The International Maritime Satellite Organization: Origins and structure

    Science.gov (United States)

    Doyle, S. E.

    1977-01-01

    The third session of the International Conference on the Establishment of an International Maritime Satellite System established the International Maritime Satellite Organization (INMARSAT) in 1976. Its main functions are to improve maritime communications via satellite, thereby facilitating more efficient emergency communications, ship management, and maritime public correspondence services. INMARSAT's aims are similar to those of the Intergovernmental Maritime Consultative Organization (IMCO), the main United Nations organization dealing with maritime affairs. The specific functions of INMARSAT have been established by an Intersessional Working Group (IWG) which met three times between general conference meetings. Initial investment shares for the creation of INMARSAT were shared by the United States (17%), the United Kingdom (12%), the U.S.S.R. (11%), Norway (9.50%), Japan (8.45%), Italy (4.37%), and France (3.50%).

  1. IMPLEMENTATION OF GREEN IT IN ORGANIZATIONS: A STRUCTURATIONAL VIEW

    Directory of Open Access Journals (Sweden)

    Décio Bittencourt Dolci

    2015-08-01

    Full Text Available Environmental sustainability has become increasingly important to businesses as a response to the rapid depletion of natural resources. Information Technology (IT in particular represents a meaningful part of the environmental issues that society has been facing. Therefore, Green IT emerges as a way of combining available resources and sustainable and economic policies, thus, generating benefits for both the environment and businesses. The purpose of this paper, hence, is to explain the dynamics of Green IT implementation in organizations in light of the structurationist view of technology. We conducted a case study research based on the cases of three Brazilian companies interested in this movement. Results provide a better understanding of the relationship among technology, individuals, and organization institutional properties, thus enhancing the role played by IT teams in institutionalizing the environmental dimension of sustainability in organizations.

  2. Identification and delineation of members of the Entamoeba complex by pyrosequencing.

    Science.gov (United States)

    Stensvold, Christen R; Lebbad, Marianne; Verweij, Jaco J; Jespersgaard, Cathrine; von Samson-Himmelstjerna, Georg; Nielsen, Susanne S; Nielsen, Henrik V

    2010-12-01

    A method using a single-round PCR coupled to pyrosequencing was developed for the detection and differentiation of members of the Entamoeba complex. The technique was evaluated using DNA isolated directly from faecal specimens and compared with a duplex real-time PCR targeting Entamoeba histolytica and Entamoeba dispar, and a conventional single-round PCR for the detection of Entamoeba moshkovskii. Tetranucleate cysts from 102 faecal specimens from Swedish, Danish and Dutch patients test-positive for the Entamoeba complex by coproscopic examination were identified to species using each of the three methods. Although none of the patients were confirmed to be positive for E. moshkovskii, E. histolytica and E. dispar were identified in 17 and 86 of the samples, respectively, one of the samples containing both species. There was concordance in results between pyrosequencing and the two other methods used. This study showed that PCR and pyrosequencing could be used for the rapid and high throughput identification of Entamoeba species.

  3. Development of pyrosequencing methods for the rapid detection of RAS mutations in clinical samples.

    Science.gov (United States)

    Cortes, Ulrich; Guilloteau, Karline; Rouvreau, Mélanie; Archaimbault, Céline; Villalva, Claire; Karayan-Tapon, Lucie

    2015-10-01

    In advanced colorectal carcinoma (CRC) patients, extended RAS mutations testing (KRAS exons 2 to 4 and NRAS exons 2 to 4) is a prerequisite for patient stratification to anti-EGFr therapy. Accurately distinguishing mutant patients from potential responders has a clinically critical impact, and thus effective and low cost methods are needed for identification of the mutation status. We have developed quantitative pyrosequencing assays for sensitive and rapid detection of mutant RAS alleles in formalin-fixed, paraffin-embedded tissues. Exons 2 to 4 of KRAS and NRAS genes were PCR amplified and analyzed by pyrosequencing. For validation, PCR products were sequenced by conventional Sanger sequencing. Analytical sensitivity of these assays was determined by calculating the limit of detection. The results showed that low levels of mutant RAS alleles (2-13%) can be detected with pyrosequencing assays.

  4. Flexible organic solar cells including efficiency enhancing grating structures

    DEFF Research Database (Denmark)

    Oliveira Hansen, Roana Melina de; Liu, Yinghui; Madsen, Morten

    2013-01-01

    In this work, a new method for the fabrication of organic solar cells containing functional light-trapping nanostructures on flexible substrates is presented. Polyimide is spin-coated on silicon support substrates, enabling standard micro- and nanotechnology fabrication techniques......, such as photolithography and electron-beam lithography, besides the steps required for the bulk-heterojunction organic solar cell fabrication. After the production steps, the solar cells on polyimide are peeled off the silicon support substrates, resulting in flexible devices containing nanostructures for light absorption...

  5. Organic structures design applications in optical and electronic devices

    CERN Document Server

    Chow, Tahsin J

    2014-01-01

    ""Presenting an overview of the syntheses and properties of organic molecules and their applications in optical and electronic devices, this book covers aspects concerning theoretical modeling for electron transfer, solution-processed micro- and nanomaterials, donor-acceptor cyclophanes, molecular motors, organogels, polyazaacenes, fluorogenic sensors based on calix[4]arenes, and organic light-emitting diodes. The publication of this book is timely because these topics have become very popular nowadays. The book is definitely an excellent reference for scientists working in these a

  6. Structural organization of mammalian prions as probed by limited proteolysis

    Science.gov (United States)

    The GPI- transgenic mouse model was used to study the structure of GPI- prions. We obtained valuable information about the structure of prions by performing limited proteolysis of the GPI- prions and analyzing the results by mass spectrometry and Western blot. This information coupled with previous ...

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

    DEFF Research Database (Denmark)

    Rasmussen, Ole Horn

    of an institutional economic explanation. On the other side, the theoretical analysis of the process of agricultural structural change indicates a theoretical agreement concerning the result of the process. The dissertation illustrates how Veblen and Cochrane, from different theoretical apparatuses, generally agree...... the general economic structural change. This makes the idea of understanding organic agriculture by itself or even as part of agriculture inadequate. Organic agriculture must be perceived as forming part of the general social economy. We find that the Veblenian concept of the process of structural change....... Such is the objective structural economic framework in which the organic agriculture phenomenon evolves. When we analyse organic agriculture versus conventional agriculture, we get indications that organic agriculture has disadvantages in the process of agricultural structural change compared with conventional...

  8. High-speed prediction of crystal structures for organic molecules

    Science.gov (United States)

    Obata, Shigeaki; Goto, Hitoshi

    2015-02-01

    We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

  9. Performance of Different Analytical Software Packages in Quantification of DNA Methylation by Pyrosequencing

    Science.gov (United States)

    Grasso, Chiara; Trevisan, Morena; Fiano, Valentina; Tarallo, Valentina; De Marco, Laura; Sacerdote, Carlotta; Richiardi, Lorenzo; Merletti, Franco; Gillio-Tos, Anna

    2016-01-01

    Background Pyrosequencing has emerged as an alternative method of nucleic acid sequencing, well suited for many applications which aim to characterize single nucleotide polymorphisms, mutations, microbial types and CpG methylation in the target DNA. The commercially available pyrosequencing systems can harbor two different types of software which allow analysis in AQ or CpG mode, respectively, both widely employed for DNA methylation analysis. Objective Aim of the study was to assess the performance for DNA methylation analysis at CpG sites of the two pyrosequencing software which allow analysis in AQ or CpG mode, respectively. Despite CpG mode having been specifically generated for CpG methylation quantification, many investigations on this topic have been carried out with AQ mode. As proof of equivalent performance of the two software for this type of analysis is not available, the focus of this paper was to evaluate if the two modes currently used for CpG methylation assessment by pyrosequencing may give overlapping results. Methods We compared the performance of the two software in quantifying DNA methylation in the promoter of selected genes (GSTP1, MGMT, LINE-1) by testing two case series which include DNA from paraffin embedded prostate cancer tissues (PC study, N = 36) and DNA from blood fractions of healthy people (DD study, N = 28), respectively. Results We found discrepancy in the two pyrosequencing software-based quality assignment of DNA methylation assays. Compared to the software for analysis in the AQ mode, less permissive criteria are supported by the Pyro Q-CpG software, which enables analysis in CpG mode. CpG mode warns the operators about potential unsatisfactory performance of the assay and ensures a more accurate quantitative evaluation of DNA methylation at CpG sites. Conclusion The implementation of CpG mode is strongly advisable in order to improve the reliability of the methylation analysis results achievable by pyrosequencing. PMID

  10. Performance of Different Analytical Software Packages in Quantification of DNA Methylation by Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Chiara Grasso

    Full Text Available Pyrosequencing has emerged as an alternative method of nucleic acid sequencing, well suited for many applications which aim to characterize single nucleotide polymorphisms, mutations, microbial types and CpG methylation in the target DNA. The commercially available pyrosequencing systems can harbor two different types of software which allow analysis in AQ or CpG mode, respectively, both widely employed for DNA methylation analysis.Aim of the study was to assess the performance for DNA methylation analysis at CpG sites of the two pyrosequencing software which allow analysis in AQ or CpG mode, respectively. Despite CpG mode having been specifically generated for CpG methylation quantification, many investigations on this topic have been carried out with AQ mode. As proof of equivalent performance of the two software for this type of analysis is not available, the focus of this paper was to evaluate if the two modes currently used for CpG methylation assessment by pyrosequencing may give overlapping results.We compared the performance of the two software in quantifying DNA methylation in the promoter of selected genes (GSTP1, MGMT, LINE-1 by testing two case series which include DNA from paraffin embedded prostate cancer tissues (PC study, N = 36 and DNA from blood fractions of healthy people (DD study, N = 28, respectively.We found discrepancy in the two pyrosequencing software-based quality assignment of DNA methylation assays. Compared to the software for analysis in the AQ mode, less permissive criteria are supported by the Pyro Q-CpG software, which enables analysis in CpG mode. CpG mode warns the operators about potential unsatisfactory performance of the assay and ensures a more accurate quantitative evaluation of DNA methylation at CpG sites.The implementation of CpG mode is strongly advisable in order to improve the reliability of the methylation analysis results achievable by pyrosequencing.

  11. Organizational Structures and Data Use in Volunteer Monitoring Organizations (VMOs)

    Science.gov (United States)

    Laird, Shelby Gull; Nelson, Stacy A. C.; Stubbs, Harriett S.; James, April L.; Menius, Erika

    2012-01-01

    Complex environmental problems call for unique solutions to monitoring efforts alongside developing a more environmentally literate citizenry. Community-based monitoring (CBM) through the use of volunteer monitoring organizations helps to provide a part of the solution, particularly when CBM groups work with research scientists or government…

  12. Organizing Innovation within Incumbent Firms: Structure Enabling Strategic Autonomy

    NARCIS (Netherlands)

    van Looy, Bart; van Looy, Bart; Visscher, Klaasjan

    2011-01-01

    In this paper we will discuss how large established firms can be effective in organizing innovation alongside their current business. We examine the trajectory of an incumbent firm in the telecommunication industry – Alcatel – which has been successful in exploring and exploiting the promises of

  13. Organizational Structures and Data Use in Volunteer Monitoring Organizations (VMOs)

    Science.gov (United States)

    Laird, Shelby Gull; Nelson, Stacy A. C.; Stubbs, Harriett S.; James, April L.; Menius, Erika

    2012-01-01

    Complex environmental problems call for unique solutions to monitoring efforts alongside developing a more environmentally literate citizenry. Community-based monitoring (CBM) through the use of volunteer monitoring organizations helps to provide a part of the solution, particularly when CBM groups work with research scientists or government…

  14. Organizing innovation within incumbent firms: structure enabling strategic autonomy

    NARCIS (Netherlands)

    Looy, van Bart; Visscher, Klaasjan

    2011-01-01

    In this paper we will discuss how large established firms can be effective in organizing innovation alongside their current business. We examine the trajectory of an incumbent firm in the telecommunication industry – Alcatel – which has been successful in exploring and exploiting the promises of bro

  15. 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.

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

    DEFF Research Database (Denmark)

    Inceoglu, Özgül; Abu Al-Soud, Waleed; Salles, Joana Falcão;

    2011-01-01

    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 stru......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...

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

    Directory of Open Access Journals (Sweden)

    Özgül Inceoğlu

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

  18. Pyrosequencing revealed highly microbial phylogenetic diversity in ferromanganese nodules from farmland.

    Science.gov (United States)

    Hu, Min; Li, Fangbai; Lei, Jing; Fang, Yuan; Tong, Hui; Wu, Weijian; Liu, Chengshuai

    2015-01-01

    There is renewed interest in the origin and makeup of ferromanganese nodules (FMNs), long known to soil mineralogists as unusual secondary minerals. However, new evidence suggests that microorganisms play a significant role in the generation of FMNs. The biogenic origin of nodules has remained elusive because until recently, little has been known about the overall microbial community structure in their microbiota. To learn more about the microbial community and to determine the relative abundance, diversity, and composition of the microbial communities present in FMNs and their surrounding soil, we used pyrosequencing to investigate 16S rRNA genes obtained from vertical soil profiles of both paddy fields and sugarcane fields. Using pyrotaq 16S rRNA gene sequencing, we show that the microbial phylogenetic diversity of nodules was higher than those reported in previous studies of this biosphere, and we identified many previously unidentified microorganisms. Here, we show that the microbial community of these nodules is dominated by Burkholderiales, Rhodocyclales, Acidobacteriales, Desulfuromonales, and Clostridiales, and there were no statistically significant differences found when comparing the microbial community structures of FMNs obtained from vertical soil sequences. Although the microbial composition was markedly different between the surrounding soil and the FMNs, the microbes found within the FMNs were very similar to other FMNs from both field types examined here. In addition to their geochemical properties and the microbial community composition of FMNs, we found that the levels of iron (Fe), manganese (Mn), and SiO2 greatly impact the microbial diversity among FMN communities. Our results indicate that the FMN microbial communities from different land-use types are very similar and suggest that natural selection of these microbes is based on the oligotrophic conditions and the high metal content. Researching FMNs in these two land-use patterns, which

  19. Expert system for elucidation of structures of organic compounds——Structural generator of ESESOC-II

    Institute of Scientific and Technical Information of China (English)

    胡昌玉; 许禄

    1995-01-01

    An expert system for the elucidation of the structures of organic compounds--ESESOC-IIhas been designed. It is composed of three parts: spectroscopic data analysis, structure generator, and evaluation of the candidate structures. The heart of ESESOC is the structure generator, as an integral part, which accepts the specific types of information, e.g. molecular formulae, substructure constraints, and produces an exhaustive and irredundant list of candidate structures. The scheme for the structural generation is given, in which the depth-first search strategy is used to fill the bonding adjacency matrix (BAM) and a new method is introduced to remove the duplicates.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Azhahianambi Palavesam

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

  2. Flexible organic solar cells including efficiency enhancing grating structures

    DEFF Research Database (Denmark)

    Oliveira Hansen, Roana Melina de; Liu, Yinghui; Madsen, Morten

    2013-01-01

    enhancement. Since the solar cells avoid using brittle electrodes, the performance of the flexible devices is not affected by the peeling process. We have investigated three different nanostructured grating designs and conclude that gratings with a 500 nm pitch distance have the highest light......In this work, a new method for the fabrication of organic solar cells containing functional light-trapping nanostructures on flexible substrates is presented. Polyimide is spin-coated on silicon support substrates, enabling standard micro- and nanotechnology fabrication techniques......, such as photolithography and electron-beam lithography, besides the steps required for the bulk-heterojunction organic solar cell fabrication. After the production steps, the solar cells on polyimide are peeled off the silicon support substrates, resulting in flexible devices containing nanostructures for light absorption...

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

    NARCIS (Netherlands)

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

    2012-01-01

    Aims: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Methods and Results: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was u

  4. Development of a candidate method for forensic microbial genotyping using multiplex pyrosequencing combined with a universal biotinylated primer.

    Science.gov (United States)

    Gu, Yan; Mao, Xuhu; Zha, Lagabaiyila; Hou, Yiping; Yun, Libing

    2015-01-01

    Bacterial genotyping can be used for crime scene investigations and contribute to the attribution of biological attacks for microbial forensics. PyroMark ID Pyrosequencer as an accurate detection platform for single nucleotide polymorphisms (SNPs) has been applied to identify and resolve microorganisms involved in closely Escherichia coli O157:H7 (E. coli O157:H7). To explore more applications and improve the efficiency for pyrosequencing in this field, we developed a method integrated multiplex pyrosequencing with a universal primer. Two multiplex pyrosequencing assays with a universal biotinylated primer were designed to analyze five SNPs located in four gene of E. coli O157:H7 strain. The accuracy of the established assays was validated by genotyping reference strain E. coli O157:H7 EDL933 and E. coli K-12. We also demonstrated that two multiplex pyrosequencing assays were specific and sensitive for genotyping closely related E. coli O157 strains. Reproducibility of results and multiplexing capability were evaluated by a comparison of this method with the monoplex pyrosequencing. Furthermore, these two multiplex pyrosequencing assays have been successfully applied to detect 11 E. coli O157 strains isolated from 1504 Chinese livestock samples. This method reduces costs and time consumption in the process of pyrosequencing analysis, and potentially serves as a rapid tool and reliable candidate strategy for the microbial identification and other genotyping application.

  5. Molecular evolution, intracellular organization, and the quinary structure of proteins.

    OpenAIRE

    McConkey, E H

    1982-01-01

    High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

  6. Conjugated Polymers for Organic Electronics: Structural and Electronic Characteristics

    OpenAIRE

    Rafael C. González-Cano; López Navarrete, Juan T.; Ruiz Delgado, M. Carmen

    2016-01-01

    The use of organic materials to design electronic devices has actually presented a broad interest for because they constitute an ecological and suitable resource for our current "electronic world". These materials provide several advantages (low cost, light weight, good flexibility and solubility to be easily printed) that cannot be afforded with silicium. They can also potentially interact with biological systems, something impossible with inorganic devices. Between these materials we can in...

  7. Pyrosequencing analysis of microbial communities in hollow fiber-membrane biofilm reactors system for treating high-strength nitrogen wastewater.

    Science.gov (United States)

    Park, Jung-Hun; Choi, Okkyoung; Lee, Tae-Ho; Kim, Hyunook; Sang, Byoung-In

    2016-11-01

    Wastewaters from swine farms, nitrogen-dealing industries or side-stream processes of a wastewater treatment plant (e.g., anaerobic digesters, sludge thickening processes, etc.) are characterized by low C/N ratios and not easily treatable. In this study, a hollow fiber-membrane biofilm reactors (HF-MBfR) system consisting of an O2-based HF-MBfR and an H2-based HF-MBfR was applied for treating high-strength wastewater. The reactors were continuously operated with low supply of O2 and H2 and without any supply of organic carbon for 250 d. Gradual increase of ammonium and nitrate concentration in the influent showed stable and high nitrogen removal efficiency, and the maximum ammonium and nitrate removal rates were 0.48 kg NH4(+)-N m(-3) d(-1) and 0.55 kg NO3(-)-N m(-3) d(-1), respectively. The analysis of the microbial communities using pyrosequencing analysis indicated that Nitrosospira multiformis, ammonium-oxidizing bacteria, and Nitrobacter winogradskyi and Nitrobacter vulgaris, nitrite-oxidizing bacteria were highly enriched in the O2-based HF-MBfR. In the H2-based HF-MBfR, hydrogenotrophic denitrifying bacteria belonging to the family of Thiobacillus and Comamonadaceae were initially dominant, but were replaced to heterotrophic denitrifiers belonging to Rhodocyclaceae and Rhodobacteraceae utilizing by-products induced from autotrophic denitrifying bacteria. The pyrosequencing analysis of microbial communities indicates that the autotrophic HF-MBfRs system well developed autotrophic nitrifying and denitrifying bacteria within a relatively short period to accomplish almost complete nitrogen removal.

  8. Direct-writing organic three-dimensional nanofibrous structure

    Science.gov (United States)

    Wang, Han; Zheng, Gaofeng; Li, Wenwang; Wang, Xiang; Sun, Daoheng

    2011-02-01

    Direct-writing technology based on Near-Field Electrospinning (NFES) was used to fabricate an organic three-dimensional nanofibrous circle on the patterned silicon substrate. In NFES, straight jet without splitting and chaotic motion was utilized to direct-write orderly nanofiber. When the collector movement speed was lower than electrospinning rate, the relaxed nanofiber would be lead into the pendulum motion by the electrical field force and Coulomb repulsion force from the residual charges on the collector. When the relative air humidity is lower than 35%, individual nanofiber with larger elastic resistance would reveal a good self-assembly performance. Owing to the guidance of the electric field force at the edge of the micro-pattern, a nanofiber was deposited layer by layer to format a 3D nanofibrous circle on the top surface of the micro-pattern. The dimension scale of 3D nanofibrous circle was smaller than 30 µm. With the help of a microscope, a 3D nanofibrous circle can be deposited precisely on the strip micro-pattern with width of 4 µm. Furthermore, a 3D nanofibrous circle in different shapes can be obtained by using special micro-patterns. This organic three-dimensional nanofibrous circle has created a new aspect for the fabrication of organic micro/nanosystems.

  9. Cluster-induced desorption from metal organic surfaces: Structural effects

    Energy Technology Data Exchange (ETDEWEB)

    Delcorte, A., E-mail: arnaud.delcorte@uclouvain.be [Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve (Belgium); Hoecke, E. van; Restrepo, O.A. [Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve (Belgium)

    2013-05-15

    Molecular dynamics (MD) simulations are used to model the 10 keV bombardment of Au-nanoparticle (NP)-covered polymeric samples by Ga, C{sub 60} and Au{sub 400} projectiles, at normal incidence. While the presence of the Au-NPs tends to enhance the organic material emission upon Ga and Au{sub 400} bombardment, as a result of increased projectile stopping, it strongly reduces the organic emission upon C{sub 60} bombardment because of the projectile reflection. Our results show that these trends are valid for kDa polymers (which can be emitted intact) as well as for virtually infinite length chains (which require fragmentation), but that the polymer sputtered mass is consistently >3 times larger in the case of the kDa molecules for all impact points and projectiles. Using a series of samples, it is also shown that embedding the Au-NPs in the organic material leads to completely different results, with, upon C{sub 60} bombardment, the largest sputtered masses observed for impacts above the NPs. For Au{sub 400} bombardment, the burial of the Au-NPs leads to comparatively lower sputtered masses. These new results demonstrate the complexity of the sputtering of nanostructured hybrid materials by cluster projectiles and suggest various artifacts that should complicate the analysis and depth profiling of such materials.

  10. Estudio comparativo de la estructura del bacterioplancton en aguas del Mar Argentino mediante el método de pirosecuenciación 454 tag A comparative study of bacterioplankton structure in Argentinian Sea waters by the 454 - tag pyrosequencing method

    Directory of Open Access Journals (Sweden)

    S. R. Peressutti

    2010-12-01

    Full Text Available El presente estudio brinda la primera información sobre diversidad y abundancia de las comunidades microbianas en dos ambientes del Mar Argentino obtenida mediante la técnica de pirosecuenciación tag ribosomal 454. Dentro del dominio Bacteria, se observaron más de 4 600 secuencias únicas a partir de 36 188 amplicones de tags y se identificaron 280 filotipos. Además, se detectaron cerca de 2 700 secuencias únicas a partir de más de 47 700 tags pertenecientes al dominio Archaea, lo que definió sólo 5 filotipos diferentes. La distancia de Jaccard presentó valores de 0,6 para bacterias y de 0,2 para arqueas, esto indica mayor diferencia entre las bacterias en los dos sitios. En el ambiente marino los filotipos más dominantes fueron Bacteroidetes Flavobacteriaceae, Proteobacteria Gammaproteobacteria, Proteobacteria Rhodobacteraceae y Proteobacteria Rickettsiales SAR11, mientras que en el estuario predominaron Pseudoalteromonadaceae Pseudoalteromonas, Proteobacteria Gammaproteobacteria, Proteobacteria Shewanella y Proteobacteria Rickettsiales SAR11. Los 2 filotipos de arqueas encontrados en mayor proporción fueron Archaea Euryarchaeota y Archaea Crenarchaeota. Las secuencias tag más numerosas representaron taxa caracterizados previamente, aunque también se halló un elevado número de filotipos de gran diversidad y de baja abundancia, que forman parte de la denominada "biosfera rara", aún no explorada, que pueden tener un papel ecológico crucial.The present study provides the first information about diversity and abundance of microbial communities in two environments of the Argentinian Sea by the 454 - tag pyrosequencing technique. We observed more than 4,600 unique bacterial sequences from 36,188 tag amplicons, forming 280 phylotypes. In addition, nearly 2,700 unique sequences from more than 47,700 tags identified as Archaea, defined only 5 different phylotypes. The Jaccard distance (0.6 for Bacteria and 0.2 for Archaea indicated

  11. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  12. 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

  13. Self-organization in neural networks - Applications in structural optimization

    Science.gov (United States)

    Hajela, Prabhat; Fu, B.; Berke, Laszlo

    1993-01-01

    The present paper discusses the applicability of ART (Adaptive Resonance Theory) networks, and the Hopfield and Elastic networks, in problems of structural analysis and design. A characteristic of these network architectures is the ability to classify patterns presented as inputs into specific categories. The categories may themselves represent distinct procedural solution strategies. The paper shows how this property can be adapted in the structural analysis and design problem. A second application is the use of Hopfield and Elastic networks in optimization problems. Of particular interest are problems characterized by the presence of discrete and integer design variables. The parallel computing architecture that is typical of neural networks is shown to be effective in such problems. Results of preliminary implementations in structural design problems are also included in the paper.

  14. 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.

  15. 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.

  16. Energy transfer in organic multilayer quantum well structure and its application to OLEDs

    Institute of Scientific and Technical Information of China (English)

    ZHAO De-wei; SONG Shu-fang; ZHAO Su-ling; XU Zheng

    2007-01-01

    We fabricate a series of samples and OLEDs with organic multilayer quantum well structure, which consist of alternate PBD and Alq3. Both PBD and Alq3 are electron-transporting materials, and PBD is used as potential barrier layer, while Alq3 is used as potential well layer and emitting layer. Compared with double-layer structure, the luminescent characteristics of organic samples and diodes with quantum well structure are investigated and the quantum well structure helps the energy transfer between well layer and barrier layer. The quantum well structure makes carriers disperse in the different well layers and then increases the number of excitons to enhance the efficiency of the recombination.

  17. Microbial community structure affects marine dissolved organic matter composition

    Directory of Open Access Journals (Sweden)

    Elizabeth B Kujawinski

    2016-04-01

    Full Text Available Marine microbes are critical players in the global carbon cycle, affecting both the reduction of inorganic carbon and the remineralization of reduced organic compounds back to carbon dioxide. Members of microbial consortia all depend on marine dissolved organic matter (DOM and in turn, affect the molecules present in this heterogeneous pool. Our understanding of DOM produced by marine microbes is biased towards single species laboratory cultures or simplified field incubations, which exclude large phototrophs and protozoan grazers. Here we explore the interdependence of DOM composition and bacterial diversity in two mixed microbial consortia from coastal seawater: a whole water community and a <1.0-μm community dominated by heterotrophic bacteria. Each consortium was incubated with isotopically-labeled glucose for 9 days. Using stable-isotope probing techniques and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry, we show that the presence of organisms larger than 1.0-μm is the dominant factor affecting bacterial diversity and low-molecular-weight (<1000 Da DOM composition over this experiment. In the <1.0-μm community, DOM composition was dominated by compounds with lipid and peptide character at all time points, confirmed by fragmentation spectra with peptide-containing neutral losses. In contrast, DOM composition in the whole water community was nearly identical to that in the initial coastal seawater. These differences in DOM composition persisted throughout the experiment despite shifts in bacterial diversity, underscoring an unappreciated role for larger microorganisms in constraining DOM composition in the marine environment.

  18. 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…

  19. 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…

  20. Monitoring Scientific Developments from a Dynamic Perspective: Self-Organized Structuring To Map Neural Network Research.

    Science.gov (United States)

    Noyons, E. C. M.; van Raan, A. F. J.

    1998-01-01

    Using bibliometric mapping techniques, authors developed a methodology of self-organized structuring of scientific fields which was applied to neural network research. Explores the evolution of a data generated field structure by monitoring the interrelationships between subfields, the internal structure of subfields, and the dynamic features of…

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

    NARCIS (Netherlands)

    Meijaard, J.; Uhlaner, L.M.

    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

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

    NARCIS (Netherlands)

    Meijaard, J.; Uhlaner, L.M.

    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

  3. Pashtun Social Structure: Cultural Perceptions and Segmentary Lineage Organization

    Science.gov (United States)

    2011-08-03

    The Pashtun are an ethnic group that straddles the Afghanistan-Pakistan border, and are the largest group in Afghanistan. Pashtun social structure is...proceeding upward through various levels to an entire ethnic group . These relationships are based on kinship and shared culture. Segmentary lineage

  4. Structural Characterization and Toxicity Prediction of Some Organic Compounds

    Institute of Scientific and Technical Information of China (English)

    LIAO Li-Mia; LI Jian-Feng; WANG Bi

    2011-01-01

    A new molecular structural characterization(MSC)method called molecular vertexes correlative index(MVCI)was constructed in this paper.The index was used to describe the structures of 45 compounds and a quantitative structure-activity relationship(QSAR)model of toxicity(–lgEC50)was obtained through multiple linear regression(MLR)and stepwise multiple regression(SMR).The correlation coefficient(R)of the model was 0.912,and the standard deviation(SD)of the model was 0.525.The estimation stability and prediction ability of the model were strictly analyzed by both internal and external validations.The Leave-One-Out(LOO)Cross-Validation(CV)correlation coefficient(RCV)was 0.816 and the standard deviation(SDCV)was 0.739,respectively.For the external validation,the correlation coefficient(Rtest)was 0.905 and the standard deviation(SDtest)was 0.520,respectively.The results showed that the index was superior in molecular structural representation.The stability and predictability of the model were good.

  5. Structure and membrane organization of photosystem II in green plants

    NARCIS (Netherlands)

    Hankamer, B; Barber, J; Boekema, EJ

    1997-01-01

    Photosystem II (PSII) is the pigment protein complex embedded in the thylakoid membrane of higher plants, algae, and cyanobacteria that uses solar energy to drive the photosynthetic water-splitting reaction. This chapter reviews the primary, secondary, tertiary, and quaternary structures of PSII as

  6. Managing University IT Risks in Structured and Organized Environment

    Directory of Open Access Journals (Sweden)

    Sayef Sami Hassen

    2013-07-01

    Full Text Available In this digital era, most universities rely heavily on Information Technology (IT to process their information for better support of their visions and missions. However, with this reliance, IT is facing different types of risks under expansions and complexities as experienced by most universities these days. IT risk is not bounded to only information systems and security, but unbounded to encompass the risk to financial, strategic, technological, as well as reputational. All these types of risk are prevalent in universities and hence the need to implement an effective risk management process including but not limited to IT. The best opportunities for managing IT risks can be achieved through managing it within an integrated approach and not to be carried out separately from managing risks of the organization. Such approach ensures that IT is achieving the goals and objectives of the organization by providing a reasonable basis for strategic planning and improves decision making for top management based on risk management value. This study identifies the current implementation of risk management at one Malaysian university to face all risks. The main findings of this study are: (1 The majority of staff supports the fundamental objectives of risk management; (2 The necessity to improve and enhance some procedures of risk management at the university. This study provide recommendations and improvements in some procedures of risk management to increase the awareness of risk management among all the university staff.

  7. Cellular self-organization on micro-structured surfaces.

    Science.gov (United States)

    Röttgermann, Peter J F; Alberola, Alicia Piera; Rädler, Joachim O

    2014-04-14

    Micro-patterned surfaces are frequently used in high-throughput single-cell studies, as they allow one to image isolated cells in defined geometries. Commonly, cells are seeded in excess onto the entire chip, and non-adherent cells are removed from the unpatterned sectors by rinsing. Here, we report on the phenomenon of cellular self-organization, which allows for autonomous positioning of cells on micro-patterned surfaces over time. We prepared substrates with a regular lattice of protein-coated adhesion sites surrounded by PLL-g-PEG passivated areas, and studied the time course of cell ordering. After seeding, cells randomly migrate over the passivated surface until they find and permanently attach to adhesion sites. Efficient cellular self-organization was observed for three commonly used cell lines (HuH7, A549, and MDA-MB-436), with occupancy levels typically reaching 40-60% after 3-5 h. The time required for sorting was found to increase with increasing distance between adhesion sites, and is well described by the time-to-capture in a random-search model. Our approach thus paves the way for automated filling of cell arrays, enabling high-throughput single-cell analysis of cell samples without losses.

  8. Flexible organic solar cells including efficiency enhancing grating structures

    Science.gov (United States)

    Melina de Oliveira Hansen, Roana; Liu, Yinghui; Madsen, Morten; Rubahn, Horst-Günter

    2013-04-01

    In this work, a new method for the fabrication of organic solar cells containing functional light-trapping nanostructures on flexible substrates is presented. Polyimide is spin-coated on silicon support substrates, enabling standard micro- and nanotechnology fabrication techniques, such as photolithography and electron-beam lithography, besides the steps required for the bulk-heterojunction organic solar cell fabrication. After the production steps, the solar cells on polyimide are peeled off the silicon support substrates, resulting in flexible devices containing nanostructures for light absorption enhancement. Since the solar cells avoid using brittle electrodes, the performance of the flexible devices is not affected by the peeling process. We have investigated three different nanostructured grating designs and conclude that gratings with a 500 nm pitch distance have the highest light-trapping efficiency for the selected active layer material (P3HT:PCBM), resulting in an enhancement of about 34% on the solar cell efficiency. The presented method can be applied to a large variety of flexible nanostructured devices in future applications.

  9. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing.

    Science.gov (United States)

    Kim, Keun-Sik; Noh, Choong Hwan; Moon, Shin-Joo; Han, Seung-Hee; Bang, In-Chul

    2016-06-01

    Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.

  10. Development and multiplexing of microsatellite markers using pyrosequencing in the clonal plant Comarum palustre (Rosaceae).

    Science.gov (United States)

    Somme, L; Raabová, J; Jacquemart, A L; Raspé, O

    2012-01-01

    Microsatellites represent one of the most commonly used genetic markers for population genetic studies. Traditionally, their development is quite time consuming, requiring construction of a genomic library enriched for repeated motifs. Using pyrosequencing, a fast and cost-effective new generation sequencing technique, we produced 24,340,862 bases in 63,860 short fragment reads, including 1170 dinucleotide motifs with a minimum of six repeats and 1383 trinucleotide motifs with a minimum of four repeats for the Marsh Cinquefoil, Comarum palustre L., an endangered marsh pioneer species. We selected 58 loci with SSR (Short Sequence Repeat) segments (at least 10 repeats) for a preliminary screening. Out of them, we screened 29 loci on a capillary sequencer after ligation in a vector and PCR using T7 forward primer labelled with FAM fluorescent dye and the specific unlabeled reverse primers. This procedure allowed us to screen large number of candidate loci with the same labelled primer and unlabelled specific primers. Finally, we characterized 20 polymorphic microsatellite markers, nine dinucleotides and 11 trinucleotides. We used these markers to assess genetic diversity and clonal structure in two Belgian populations. All loci showed a maximum of two alleles per individual, suggesting that they are from a diploid genome. One genet was detected in a newly extending population while 53 different genets in a long-term ecologically managed population. The number of alleles per locus ranged from 6 to 14 in this old population with an expected heterozygosity, ranging from 0.5964 to 0.8278. These preliminary results show a genet size up to 7.2 m.

  11. Structure of Solvent-Free Nanoparticle−Organic Hybrid Materials

    KAUST Repository

    Yu, Hsiu-Yu

    2010-11-16

    We derive the radial distribution function and the static structure factor for the particles in model nanoparticleorganic hybrid materials composed of nanoparticles and attached oligomeric chains in the absence of an intervening solvent. The assumption that the oligomers form an incompressible fluid of bead-chains attached to the particles that is at equilibrium for a given particle configuration allows us to apply a density functional theory for determining the equilibrium configuration of oligomers as well as the distribution function of the particles. A quasi-analytic solution is facilitated by a regular perturbation analysis valid when the oligomer radius of gyration R g is much greater than the particle radius a. The results show that the constraint that each particle carries its own share of the fluid attached to itself yields a static structure factor that approaches zero as the wavenumber approaches zero. This result indicates that each particle excludes exactly one other particle from its neighborhood. © 2010 American Chemical Society.

  12. Thermal effect on structure organizations in cobalt-fullerene nanocomposition.

    Science.gov (United States)

    Lavrentiev, Vasily; Vacik, Jiri; Naramoto, Hiroshi; Sakai, Seiji

    2010-04-01

    Effect of deposition temperature (Ts) on structure of Co-C60 nanocomposite (NC) prepared by simultaneous deposition of cobalt and fullerene on sapphire is presented. The NC structure variations with Ts increasing from room temperature (RT) to 400 degrees C have been analyzed using scanning electron microscopy (SEM), atomic force microscopy (AFM) and Raman spectroscopy. AFM and SEM show granule-like structure of the Co-C60 film. The mixture film deposited at RT includes the hills on the surface suggesting accumulation of internal stress during phase separation. Raman spectra show 25 cm(-1) downshift of Ag(2) C60 peak suggesting -Co-C60- polymerization in C60-based matrix of the NC film. Analysis of Raman spectra has revealed existence of amorphous carbon (a-C) in the NC matrix that argues C60 decomposition. The Ts increase to 200 degrees C causes the surface hills smoothing. In parallel, downshift of the Ag(2) peak decreases to 16 cm(-1) that implies more pronounced phase separation and lower -Co-C60- polymerization efficiency. Also, amount of a-C content slightly increases. Further Ts increasing to 400 degrees C changes the NC structure dramatically. AFM shows evident enlargement of the granules. According to Raman spectra the high Ts deposition yields pronounced C60 decomposition increasing the a-C content. Features of a-C Raman peak imply nucleation of graphitic islands at the NC interfaces. Abundant decomposition of C60 in the mixture film deposited at 400 degrees C is referred to cobalt catalytic effect.

  13. Real-time PCR and pyrosequencing for differentiation of medically relevant Bartonella species.

    Science.gov (United States)

    Buss, Sarah N; Gebhardt, Linda L; Musser, Kimberlee A

    2012-11-01

    Multiple Bartonella species cause disease in humans. Although fast and accurate species differentiation could inform effective treatment interventions, species-level diagnosis of Bartonella infections is not typical. Here we describe a real-time PCR and pyrosequencing based algorithm for rapid differentiation of at least 11 medically relevant Bartonella spp.

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

    Science.gov (United States)

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

    2013-09-01

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

  15. 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...

  16. Pyrosequencing reveal distinct bacteria are carried in different wind eroded sediments from the same soil

    Science.gov (United States)

    Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. A novel technique, named pyrosequencing, promises to expand our understanding of the vast microbial diversity of soils and eroded sediments as it can sequence between...

  17. Pyrosequencing for rapid detection of Mycobacterium tuberculosis second-line drugs and ethambutol resistance.

    Science.gov (United States)

    Lacoma, Alicia; Molina-Moya, Barbara; Prat, Cristina; Pimkina, Edita; Diaz, Jessica; Dudnyk, Andriy; García-Sierra, Nerea; Haba, Lucía; Maldonado, Jose; Samper, Sofia; Ruiz-Manzano, Juan; Ausina, Vicente; Dominguez, Jose

    2015-11-01

    The aim of this work was to study the diagnostic accuracy of pyrosequencing to detect resistance to fluoroquinolones, kanamycin, amikacin, capreomycin, and ethambutol (EMB) in Mycobacterium tuberculosis clinical strains. One hundred four clinical isolates previously characterized by BACTEC 460TB/MGIT 960 were included. Specific mutations were targeted in gyrA, rrs, eis promoter, and embB. When there was a discordant result between BACTEC and pyrosequencing, Genotype MTBDRsl (Hain Lifescience, Nehren, Germany) was performed. Sensitivity and specificity of pyrosequencing were 70.6% and 100%, respectively, for fluoroquinolones; 93.3% and 81.7%, respectively, for kanamycin; 94.1% and 95.9%, respectively, for amikacin; 90.0% and 100%, respectively, for capreomycin; and 64.8% and 87.8%, respectively, for EMB. This study shows that pyrosequencing may be a useful tool for making early decisions regarding second-line drugs and EMB resistance. However, for a correct management of patients with suspected extensively drug-resistant tuberculosis, susceptibility results obtained by molecular methods should be confirmed by a phenotypic method.

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

    NARCIS (Netherlands)

    Inceoğlu, Özgül; Al-Soud, Waleed Abu; Salles, Joana Falcão; Semenov, Alexander V; van Elsas, Jan Dirk

    2011-01-01

    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 structu

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

    Science.gov (United States)

    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 ...

  20. Absolute Quantitation of DNA Methylation of 28 Candidate Genes in Prostate Cancer Using Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Nataڑa Vasiljeviš

    2011-01-01

    Full Text Available Aberrant DNA methylation plays a pivotal role in carcinogenesis and its mapping is likely to provide biomarkers for improved diagnostic and risk assessment in prostate cancer (PCa. We quantified and compared absolute methylation levels among 28 candidate genes in 48 PCa and 29 benign prostate hyperplasia (BPH samples using the pyrosequencing (PSQ method to identify genes with diagnostic and prognostic potential.

  1. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

    Directory of Open Access Journals (Sweden)

    Elianne Egge

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

  2. 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.

  3. The Governance Structure and Performance of Agricultural Cooperative Economic Organizations in the Three Gorges Reservoir Area

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    On the basis of questionnaire survey results of 100 agricultural cooperative economic organizations in Three Gorges Reservoir Area,this article uses the structural equation modeling as analysis tool to conduct empirical analysis of the governance structure and performance of agricultural cooperative economic organizations. The results show that the ownership structure has the most critical impact on the performance of cooperative organizations,and the impact coefficient is as high as 0.92; the importance of oversight mechanism is basically equivalent to that of the council structure for cooperative organizations,and the impact coefficient is 0.87 and 0.86,respectively,second only to the ownership structure; the size of members’ quit capacity also has a very important impact on the performance of organizations,with impact coefficient of 0.74. Thus,the problems influencing the performance of organizations,in the current governance structure of agricultural cooperative economic organizations in Three Gorges Reservoir Area,are pointed out. Finally,corresponding countermeasures are put forward.

  4. [Structural organization of 5S ribosomal DNA of Rosa rugosa].

    Science.gov (United States)

    Tynkevych, Iu O; Volkov, R A

    2014-01-01

    In order to clarify molecular organization of the genomic region encoding 5S rRNA in diploid species Rosa rugosa several 5S rDNA repeated units were cloned and sequenced. Analysis of the obtained sequences revealed that only one length variant of 5S rDNA repeated units, which contains intact promoter elements in the intergenic spacer region (IGS) and appears to be transcriptionally active is present in the genome. Additionally, a limited number of 5S rDNA pseudogenes lacking a portion of coding sequence and the complete IGS was detected. A high level of sequence similarity (from 93.7 to 97.5%) between the IGS of major 5S rDNA variants of East Asian R. rugosa and North American R. nitida was found indicating comparatively recent divergence of these species.

  5. Self-organization of punishment in structured populations

    CERN Document Server

    Perc, Matjaz

    2012-01-01

    Cooperation is crucial for the remarkable evolutionary success of the human species. Not surprisingly, some individuals are willing to bare additional costs in order to punish defectors. Current models assume that, once set, the fine and cost of punishment do not change over time. Here we show that relaxing this assumption by allowing players to adapt their sanctioning efforts in dependence on the success of cooperation can explain both, the spontaneous emergence of punishment, as well as its ability to deter defectors and those unwilling to punish them with globally negligible investments. By means of phase diagrams and the analysis of emerging spatial patterns, we demonstrate that adaptive punishment promotes public cooperation either through the invigoration of spatial reciprocity, the prevention of the emergence of cyclic dominance, or through the provision of competitive advantages to those that sanction antisocial behavior. Presented results indicate that the process of self-organization significantly e...

  6. Nanoscale Structure Of Organic Matter Explain Its Recalcitrance To Degradation

    Science.gov (United States)

    Spagnol, M.; Salati, S.; Papa, G.; Tambone, F.; Adani, F.

    2009-04-01

    Recalcitrance can be defined as the natural resistance of organic matter (OM) to microbial and enzymatic deconstruction (Himmel et al., 2007). The nature of OM recalcitrance remained not completely understood and more studies need above all to elucidate the role of the chemical topography of the OM at nanometer scale. Hydrolytic enzymes responsible of OM degradation have a molecular weight of 20-25 kD, corresponding to a size of about 4 nm, hardly penetrate into micropores (i.e. the pore having a diameter Foust, T.D. Sci. 2007, 315, 804-807. Chesson, A. In Driven by nature Plant Litter Quality and Decomposition. Cadisch, G.; Giller, K.E. Eds.; CAB International: Wallinford, UK 1997, pp 47-66. Zimmerman, A.R.; Goyne, K.W.; Chorover, J, Komarneni, S.; Brantley, S.L. Org Geochem. 2004, 35, 355-375.

  7. Organization structure and the performance of hospital emergency services.

    Science.gov (United States)

    Georgopoulos, B S

    1985-07-01

    A comparative study of 30 hospital emergency departments (EDs) and nearly 1,500 individuals associated with them was conducted. Data were obtained from institutional records, physicians, patients, and other sources. The object was to investigate the relationship between the organization and performance of these health service systems. The study assessed the quality of medical care, the quality of nursing care, and the economic efficiency of hospital EDs. The results show substantial interinstitutional differences in these criteria. They also show a significant relationship between medical and nursing care, but not between the quality of care and economic efficiency. Differences in ED performance are related to medical staffing patterns, medical teaching affiliation, personnel training, scope of emergency services, number of patient visits processed, and hospital size and complexity. Not all of these variables, however, correlate positively with all three criteria of performance, nor are they equally important to each.

  8. A novel organic-inorganic hybrid tandem solar cell with inverted structure

    Science.gov (United States)

    Bahrami, A.; Faez, R.

    2017-04-01

    A novel organic-inorganic hybrid tandem solar cell with inverted structure is proposed. This efficient double-junction hybrid tandem solar cell consists of a single-junction hydrogenated amorphous silicon (a-Si:H) subcell with n-i-p structure as front cell and a P3HT:PCBM organic subcell with inverted structure as back cell. In order to optimize the hybrid tandem cell, we have performed a simulation based on transfer matrix method. We have compared the characteristics of this novel structure with a conventional structure. As a result, a power conversion efficiency (PCE) of 6.1 and 24% improvement compared to the conventional hybrid tandem cell was achieved. We also discuss the high potential of this novel structure for realizing high-stability organic-inorganic hybrid photovoltaic devices.

  9. The impact of powder diffraction on the structural characterization of organic crystalline materials.

    Science.gov (United States)

    Tremayne, Maryjane

    2004-12-15

    The bulk properties of organic crystalline materials depend on their molecular and crystal structures but, as many of these materials cannot be prepared in a suitable form for conventional single-crystal diffraction studies, structural characterization and rationalization of these properties must be obtained from powder diffraction data. The recent development of direct-space structure solution methods has enabled the study of a wide range of organic materials using powder diffraction data, many of structural complexity only made tractable by these advances in methodology. These direct-space methods are based on a number of global optimization techniques including Monte Carlo, simulated annealing, genetic algorithm and differential evolution approaches. In this article, the implementation and relative efficiency and reliability of these methods are discussed, and their impact on the structural study of organic materials is illustrated by examples of polymorphic systems, pharmaceutical, pigment and polypeptide structures and compounds used in the study of intermolecular networks.

  10. A comparison of the capital structures of nonprofit and proprietary health care organizations.

    Science.gov (United States)

    Trussel, John

    2012-01-01

    The relative amount of debt used by an organization is an important determination of the organization's likelihood of financial problems and its cost of capital. This study addresses whether or not there are any differences between proprietary and nonprofit health care organizations in terms of capital structure. Controlling for profitability, risk, growth, and size, analysis of covariance is used to determine whether or not proprietary and nonprofit health care organizations use the same amount of leverage in their capital structures. The results indicate that there is no difference in the amount of leverage between the two institutional types. Although nonprofit and proprietary organizations have unique financing mechanisms, these differences do not impact the relative amount of debt and equity in their capital structures.

  11. Occurrence, formation and function of organic sheets in the mineral tube structures of Serpulidae (polychaeta, Annelida.

    Directory of Open Access Journals (Sweden)

    Olev Vinn

    Full Text Available A scanning electron microscopy study of organic sheets in serpulid tube mineral structures was carried out to discern their function, formation and evolution. The organic sheets may have some taxonomic value in distinguishing the two major clades of serpulids previously identified. The organic sheets in the mineral tube structure occur only in certain taxa belonging to clade A, but not all species in clade A have them. Organic sheets are best developed in genus Spirobranchus. One could speculate that organic sheets have evolved as an adaption to further strengthen the mechanical properties of the tubes in clade A, which contains serpulids with the most advanced mineral tube microstructures. The organic sheets are presumably secreted with at least some mineral phase.

  12. MGMT promoter methylation in gliomas-assessment by pyrosequencing and quantitative methylation-specific PCR

    Directory of Open Access Journals (Sweden)

    Håvik Annette

    2012-03-01

    Full Text Available Abstract Background Methylation of the O6-methylguanine-DNA methyltransferase (MGMT gene promoter is a favorable prognostic factor in glioblastoma patients. However, reported methylation frequencies vary significantly partly due to lack of consensus in the choice of analytical method. Method We examined 35 low- and 99 high-grade gliomas using quantitative methylation specific PCR (qMSP and pyrosequencing. Gene expression level of MGMT was analyzed by RT-PCR. Results When examined by qMSP, 26% of low-grade and 37% of high-grade gliomas were found to be methylated, whereas 97% of low-grade and 55% of high-grade gliomas were found methylated by pyrosequencing. The average MGMT gene expression level was significantly lower in the group of patients with a methylated promoter independent of method used for methylation detection. Primary glioblastoma patients with a methylated MGMT promoter (as evaluated by both methylation detection methods had approximately 5 months longer median survival compared to patients with an unmethylated promoter (log-rank test; pyrosequencing P = .02, qMSP P = .06. One third of the analyzed samples had conflicting methylation results when comparing the data from the qMSP and pyrosequencing. The overall survival analysis shows that these patients have an intermediate prognosis between the groups with concordant MGMT promoter methylation results when comparing the two methods. Conclusion In our opinion, MGMT promoter methylation analysis gives sufficient prognostic information to merit its inclusion in the standard management of patients with high-grade gliomas, and in this study pyrosequencing came across as the better analytical method.

  13. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  14. Cleave to Leave : Structural Insights into the Dynamic Organization of the Nuclear Pore Complex

    NARCIS (Netherlands)

    Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Rout, Michael P.

    2002-01-01

    A detailed understanding of the fine structure of the nuclear pore complex has remained elusive. Now, studies on a small protein domain have shed light on the dynamic organization of this massive assembly.

  15. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  16. Structure and organization of phospholipid/polysaccharide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Gerelli, Y; Bari, M T Di; Deriu, A [Dipartimento di Fisica and CNISM, Universita degli Studi di Parma and CRS SOFT, INFM-CNR (Italy); Cantu, L [Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina-LITA, Universita di Milano (Italy); Colombo, P; Como, C; Motta, S; Sonvico, F [Dipartimento Farmaceutico, Universita degli Studi di Parma (Italy); May, R [Institut Laue-Langevin, Grenoble (France)], E-mail: Antonio.Deriu@fis.unipr.it

    2008-03-12

    In recent years nanoparticles and microparticles composed of polymeric or lipid material have been proposed as drug carriers for improving the efficacy of encapsulated drugs. For the production of these systems different materials have been proposed, among them phospholipids and polysaccharides due to their biocompatibility, biodegradability, low cost and safety. We report here a morphological and structural investigation, performed using cryo-TEM, static light scattering and small angle neutron and x-ray scattering, on phospholipid/saccharide nanoparticles loaded with a lipophilic positively charged drug (tamoxifen citrate) used in breast cancer therapy. The lipid component was soybean lecithin; the saccharide one was chitosan that usually acts as an outer coating increasing vesicle stability. The microscopy and scattering data indicate the presence of two distinct nanoparticle families: uni-lamellar vesicles with average radius 90 A and multi-lamellar vesicles with average radius 440 A. In both families the inner core is occupied by the solvent. The presence of tamoxifen gives rise to a multi-lamellar structure of the lipid outer shell. It also induces a positive surface charge into the vesicles, repelling the positively charged chitosan molecules which therefore do not take part in nanoparticle formation.

  17. RNA structures, genomic organization and selection of recombinant HIV.

    Science.gov (United States)

    Simon-Loriere, Etienne; Rossolillo, Paola; Negroni, Matteo

    2011-01-01

    Recombination is an evolutionary mechanism intrinsic to the evolution of many RNA viruses. In retroviruses and notably in the case of HIV, recombination is so frequent that it can be considered as part of its mode of replication. This process not only plays a central role in shaping HIV genetic diversity worldwide, but has also been involved in immune escape and development of resistance to antiviral treatments. Recombination does not create new mutations in the existing genetic repertoire of the virus, but creates new combinations of pre-existing polymorphisms. The simultaneous insertion of multiple substitutions in a single replication cycle leaves little room for the progressive coevolution of regions of proteins, RNA or, more in general, genomes, to accommodate these drastic sequence changes. Therefore, recombination, while allowing the virus to rapidly explore larger sequence space than the slow accumulation of point mutations, also runs the risk of generating non functional viruses. Recombination is the consequence of a switch in the template used during reverse transcription and is promoted by the presence of structured regions in the genomic RNA template. In this review, we discuss new observations suggesting that the distribution of RNA structures along the HIV genome may enhance recombination rates in regions where the resultant progeny is less likely to be impaired, and could therefore maximize the evolutionary value of this source of genetic diversity.

  18. Direct measurement of riverine particulate organic carbon age structure

    Science.gov (United States)

    Rosenheim, Brad E.; Galy, Valier

    2012-10-01

    Carbon cycling studies focusing on transport and transformation of terrigenous carbon sources toward marine sedimentary sinks necessitate separation of particulate organic carbon (OC) derived from many different sources and integrated by river systems. Much progress has been made on isolating and characterizing young biologically-formed OC that is still chemically intact, however quantification and characterization of old, refractory rock-bound OC has remained troublesome. Quantification of both endmembers of riverine OC is important to constrain exchanges linking biologic and geologic carbon cycles and regulating atmospheric CO2 and O2. Here, we constrain petrogenic OC proportions in suspended sediment from the headwaters of the Ganges River in Nepal through direct measurement using ramped pyrolysis radiocarbon analysis. The unique results apportion the biospheric and petrogenic fractions of bulk particulate OC and characterize biospheric OC residence time. Compared to the same treatment of POC from the lower Mississippi-Atchafalaya River system, contrast in age spectra of the Ganges tributary samples illustrates the difference between small mountainous river systems and large integrative ones in terms of the global carbon cycle.

  19. Cloud motions on Venus - Global structure and organization

    Science.gov (United States)

    Limaye, S. S.; Suomi, V. E.

    1981-01-01

    Results on cloud motions on Venus obtained over a period of 3.5 days from Mariner 10 television images are presented. The implied atmosphere flow is almost zonal everywhere on the visible disk, and is in the same retrograde sense as the solid planet. Objective analysis of motions suggests the presence of jet cores (-130 m/s) and organized atmospheric waves. The longitudinal mean meridional profile of the zonal component of motion of the ultraviolet features shows presence of a midlatitude jet stream (-110 m/s). The mean zonal component is -97 m/s at the equator. The mean meridional motion at most latitudes is directed toward the pole in either hemisphere and is at least an order of magnitude smaller so that the flow is nearly zonal. A tentative conclusion from the limited coverage available from Mariner 10 is that at the level of ultraviolet features mean meridional circulation is the dominant mode of poleward angular momentum transfer as opposed to the eddy circulation.

  20. Self-organization of punishment in structured populations

    Science.gov (United States)

    Perc, Matjaž; Szolnoki, Attila

    2012-04-01

    Cooperation is crucial for the remarkable evolutionary success of the human species. Not surprisingly, some individuals are willing to bear additional costs in order to punish defectors. Current models assume that, once set, the fine and cost of punishment do not change over time. Here we show that relaxing this assumption by allowing players to adapt their sanctioning efforts in dependence on the success of cooperation can explain both the spontaneous emergence of punishment and its ability to deter defectors and those unwilling to punish them with globally negligible investments. By means of phase diagrams and the analysis of emerging spatial patterns, we demonstrate that adaptive punishment promotes public cooperation through the invigoration of spatial reciprocity, the prevention of the emergence of cyclic dominance, or the provision of competitive advantages to those that sanction antisocial behavior. The results presented indicate that the process of self-organization significantly elevates the effectiveness of punishment, and they reveal new mechanisms by means of which this fascinating and widespread social behavior could have evolved.

  1. 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...

  2. 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.…

  3. 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

  4. The control structure of team-based organizations : A diagnostic model for empowerment

    NARCIS (Netherlands)

    Kuipers, Benjamin; de Witte, M.C.

    2005-01-01

    This article describes a diagnostic model for empowerment in team-based organizations that portrays four dimensions of the organization's control structure: the level of routine, the nature of expertise, the level of dependence and the line of command. The combined positions of the set of job

  5. 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…

  6. 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…

  7. 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

  8. The control structure of team-based organizations : A diagnostic model for empowerment

    NARCIS (Netherlands)

    Kuipers, Benjamin; de Witte, M.C.

    2005-01-01

    This article describes a diagnostic model for empowerment in team-based organizations that portrays four dimensions of the organization's control structure: the level of routine, the nature of expertise, the level of dependence and the line of command. The combined positions of the set of job regula

  9. [Structural models of simple sense organs by the example of first metazoans].

    Science.gov (United States)

    Aronova, M Z

    2009-01-01

    Basic variants of the evolutional program for formation of simple sensor system--structural models of gravitation receptor, organ of vision, chemoreceptor organ as well as of the nervous system at early stages of the metazoan phylogenesis--are considered from results of our own morphofunctional studies and literature data.

  10. Crystal Structure of Ethanolamine 5-Nitrosalicylic Acid Organic Adduct

    Institute of Scientific and Technical Information of China (English)

    金轶; 车云霞; 魏荣敏; 郑吉民

    2004-01-01

    The title adduct (C18H24N4O12, Mr = 488.41) crystallizes in monoclinic, space group P21/c with a = 4.0514(19), b = 25.193(11), c = 10.751(5)(A), β = 95.070(8)o, V = 1093.0(9)(A)3, Z = 4, Dc = 1.484 g/cm3, F(000) = 512, μ(MoKα) = 1.26 cm-1, T = 293 K, the final R = 0.0593 and wR = 0.0862 for 956 observed reflections with I > 2(I). The compound is a 1:1 adduct of ethanolamine and 5-nitrosalicylic acid. The nitrogen atom of ethanolamine is protonated. In this crystal there exist a number of hydrogen bonds which link the ethanolamine and 5-nitrosalicylic acid molecules to form a three-dimensional infinite network structure.

  11. Nanoencapsulation of Fullerenes in Organic Structures with Nonpolar Cavities

    Science.gov (United States)

    Murthy, C. N.

    2005-01-01

    The formation of supramolecular structures, assemblies, and arrays held together by weak intermolecular interactions and non-covalent binding mimicking natural processes has been used in applications being anticipated in nanotechnology, biotechnology and the emerging field of nanomedicine. Encapsulation of C60 fullerene by cyclic molecules like cyclodextrins and calixarenes has potential for a number of applications. Similarly, biomolecules like lysozyme also have been shown to encapsulate C60 fullerene. This poster article reports the recent trends and the results obtained in the nanoencapsulation of fullerenes by biomolecules containing nonpolar cavities. Lysozyme was chosen as the model biomolecule and it was observed that there is no covalent bond formed between the bimolecule and the C60 fullerene. This was confirmed from fluorescence energy transfer studies. UV Vis studies further supported this observation that it is possible to selectively remove the C60 fullerene from the nonpolar cavity. This behavior has potential in biomedical applications

  12. Nanoencapsulation of Fullerenes in Organic Structures with Nonpolar Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Murthy, C. N. [M.S. University of Baroda, Applied Chemistry Department, Faculty of Technology and Engineering (India)

    2005-01-15

    The formation of supramolecular structures, assemblies, and arrays held together by weak intermolecular interactions and non-covalent binding mimicking natural processes has been used in applications being anticipated in nanotechnology, biotechnology and the emerging field of nanomedicine. Encapsulation of C{sub 60} fullerene by cyclic molecules like cyclodextrins and calixarenes has potential for a number of applications. Similarly, biomolecules like lysozyme also have been shown to encapsulate C{sub 60} fullerene. This poster article reports the recent trends and the results obtained in the nanoencapsulation of fullerenes by biomolecules containing nonpolar cavities. Lysozyme was chosen as the model biomolecule and it was observed that there is no covalent bond formed between the bimolecule and the C{sub 60} fullerene. This was confirmed from fluorescence energy transfer studies. UV-Vis studies further supported this observation that it is possible to selectively remove the C{sub 60} fullerene from the nonpolar cavity. This behavior has potential in biomedical applications

  13. 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.

  14. Rapid molecular identification of pathogenic yeasts by pyrosequencing analysis of 35 nucleotides of internal transcribed spacer 2.

    Science.gov (United States)

    Borman, Andrew M; Linton, Christopher J; Oliver, Debra; Palmer, Michael D; Szekely, Adrien; Johnson, Elizabeth M

    2010-10-01

    Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures.

  15. Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments

    Directory of Open Access Journals (Sweden)

    Jennifer L. Bowen

    2013-11-01

    Full Text Available Functional gene pyrosequencing is emerging as a useful tool to examine the diversity and abundance of microbes that facilitate key biogeochemical processes. One such process, denitrification, is of particular importance because it converts fixed nitrate (NO3- to N2 gas, which returns to the atmosphere. In N limited salt marshes, removal of NO3- prior to entering adjacent waters helps prevent eutrophication. Understanding the dynamics of salt marsh microbial denitrification is thus imperative for the maintenance of healthy coastal ecosystems. We used pyrosequencing of the nirS gene to examine the denitrifying community response to fertilization in experimentally enriched marsh plots. A key challenge in the analysis of sequence data derived from pyrosequencing is understanding whether small differences in gene sequences are ecologically meaningful. We apply a novel approach from information theory that determined that the optimal similarity level for clustering DNA sequences into OTUs, while still capturing the ecological complexity of the system, was 88% similarity. With this clustering, phylogenetic analysis yielded 6 dominant clades of denitrifiers, the largest of which, accounting for more than half of all the sequences collected, had no close cultured representatives. Of the 638 OTUs identified, only 11 were present in all plots and no single OTU was dominant. We did, however, find a large number of specialist OTUs that were present only in a single plot. The high degree of endemic OTUs, while accounting for a large proportion of the nirS diversity in the plots, were found in lower abundance than the generalist taxa. The proportion of specialist taxa increased with increasing supply of nutrients, suggesting that addition of fertilizer may create conditions that expand the niche space for denitrifying organisms and may enhance the genetic capacity for denitrification.

  16. Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

    The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

  17. Culture-independent characterization of bacteria and fungi in a poultry bioaerosol using pyrosequencing: a new approach.

    Science.gov (United States)

    Nonnenmann, M W; Bextine, B; Dowd, S E; Gilmore, K; Levin, J L

    2010-12-01

    Work in animal production facilities often results in exposure to organic dusts. Previous studies have documented decreases in pulmonary function and lung inflammation among workers exposed to organic dust in the poultry industry. Bacteria and fungi have been reported as components of the organic dust produced in poultry facilities. To date, little is known about the diversity and concentration of bacteria and fungi inside poultry buildings. All previous investigations have utilized culture-based methods for analysis that identify only biota cultured on selected media. The bacterial tag-encoded flexible (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded flexible (FLX) amplicon pyrosequencing (fTEFAP) are modern and comprehensive approaches for determining biodiversity of microorganisms and have not previously been used to provide characterization of exposure to microorganisms in an occupational environment. This article illustrates the potential application of this novel technique in occupational exposure assessment as well as other settings. An 8-hr area sample was collected using an Institute of Medicine inhalable sampler attached to a mannequin in a poultry confinement building. The sample was analyzed using bTEFAP and fTEFAP. Of the bacteria and fungi detected, 116 and 39 genera were identified, respectively. Among bacteria, Staphylococcus cohnii was present in the highest proportion (23%). The total inhalable bacteria concentration was estimated to be 7503 cells/m³. Among the fungi identified, Sagenomella sclerotialis was present in the highest proportion (37%). Aspergillus ochraceus and Penicillium janthinellum were also present in high proportions. The total inhalable fungi concentration was estimated to be 1810 cells/m³. These estimates are lower than what has been reported by others using standard epifluorescence microscope methods. However, no study has used non-culture-based techniques, such as bTEFAP and fTEFAP, to evaluate bacteria and

  18. Amylopectin molecular structure reflected in macromolecular organization of granular starch.

    Science.gov (United States)

    Vermeylen, Rudi; Goderis, Bart; Reynaers, Harry; Delcour, Jan A

    2004-01-01

    For lintners with negligible amylose retrogradation, crystallinity related inversely to starch amylose content and, irrespective of starch source, incomplete removal of amorphous material was shown. The latter was more pronounced for B-type than for A-type starches. The two predominant lintner populations, with modal degrees of polymerization (DP) of 13-15 and 23-27, were best resolved for amylose-deficient and A-type starches. Results indicate a more specific hydrolysis of amorphous lamellae in such starches. Small-angle X-ray scattering showed a more intense 9-nm scattering peak for native amylose-deficient A-type starches than for their regular or B-type analogues. The experimental evidence indicates a lower contrasting density within the "crystalline" shells of the latter starches. A higher density in the amorphous lamellae, envisaged by the lamellar helical model, explains the relative acid resistance of linear amylopectin chains with DP > 20, observed in lintners of B-type starches. Because amylopectin chain length distributions were similar for regular and amylose-deficient starches of the same crystal type, we deduce that the more dense (and ordered) packing of double helices into lamellar structures in amylose-deficient starches is due to a different amylopectin branching pattern.

  19. Temperature Triggered Structural Transitions in Surfactant organized Self Assemblies

    Science.gov (United States)

    Rose, J. Linet; Balamurugan, S.; Sajeevan, Ajin C.; Sreejith, Lisa

    2011-10-01

    Preparation & characterization of tunable fluids is an emerging area with potential application in many fields. Surfactants self assemble in aqueous solution to give a rich variety of phase structures, the size and shape of which can be tuned by additives like salts, alcohols, amines, aromatics etc or external stimuli such as light, temperature etc. The addition of long chain aliphatic alcohol has significant influence on the surfactant aggregation, as it promotes morphological growth of micelles. The cationic surfactant, Cetyl Trimethyl Ammonium Bromide (CTAB) with nonanol in presence of potassium bromide (KBr) shows thermo tunable viscosity behaviour and optical switching behaviour. The solution is visually observed to transform from a turbid and less viscous phase at low temperature to clear and considerably viscous phase at high temperature. Temperature induced changes in turbidity and viscosity are consistent with the transition from vesicle to worm like micelle. It is also worth emphasizing that the transition is thermo reversible, so that vesicles that are disrupted into micelles upon heating can be reformed upon cooling. The thermo tunable transition from turbid to transparent state and the concomitant changes in viscosity are promising for the use in smart windows, monitoring of tumor growth or in other stimuli based application.

  20. Molar crown inner structural organization in Javanese Homo erectus.

    Science.gov (United States)

    Zanolli, Clément

    2015-01-01

    This contribution investigates the inner organizational pattern (tooth tissue proportions and enamel-dentine junction morphology) of seven Homo erectus permanent molar crowns from the late Lower-early Middle Pleistocene Kabuh Formation of the Sangiran Dome (Central Java, Indonesia). The previous study of their external characteristics confirmed the degree of time-related structural reduction occurred in Javanese H. erectus, and also revealed a combination of nonmetric features which are rare in the Lower and early Middle Pleistocene dental record, but more frequently found in recent humans. In accordance with their outer occlusal morphology, the specimens exhibit a set of derived internal features, such as thick to hyperthick enamel, an incomplete expression of the crest patterns at the enamel-dentine junction (EDJ) level, a sharp EDJ topography. As a whole, these features differ from those expressed in some penecontemporaneous specimens/samples representing African H. erectus/ergaster and H. heidelbergensis, as well as in Neanderthals, but occur in recent human populations. Further research in virtual dental paleoanthropology to be developed at macroregional scale would clarify the polarity and intensity of the intermittent exchanges between continental and insular Southeast Asia around the Lower to Middle Pleistocene boundary, as well as should shed light on the still poorly understood longitudinal evolutionary dynamics across continental Asia.

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

    Directory of Open Access Journals (Sweden)

    Meiying Xu

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

  2. 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.

  3. 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.

  4. Methods of biomedical optical imaging: from subcellular structures to tissues and organs

    Science.gov (United States)

    Turchin, I. V.

    2016-05-01

    Optical bioimaging methods have a wide range of applications in the life sciences, most notably including the molecular resolution study of subcellular structures, small animal molecular imaging, and structural and functional clinical diagnostics of tissue layers and organs. We review fluorescent microscopy, fluorescent macroscopy, optical coherence tomography, optoacoustic tomography, and optical diffuse spectroscopy and tomography from the standpoint of physical fundamentals, applications, and progress.

  5. An investigation on a production company via the scope of Mintzberg’s adhocratic organization structure

    Directory of Open Access Journals (Sweden)

    Kerem Toker

    2013-01-01

    Full Text Available Today, the importance of innovation for enterprises, increase each passing day. As a result of globalization, enterprises are under intense competitive pressure. They have to make innovation for increasing to market share or for protecting to it at least. Non-innovative firms lose their customers and their existence is face to threat from other innovative actors in the market. Therefore firms have to design their organization structure that encourage to innovation. Mintzberg’s adhocratic organization structure was investigated in this article.  Thus, its aim of this study leads to resemblance and diversity between theory and practice via of the theoretical knowledge.  As a result of study; high degree of similarity between the application and Mintzberg’s theory, which is related to adhocratic organization structure, has been identified.Keywords: Innovation, Organizational Structure, Mintzberg, Adhocracy, Media Sector

  6. Hydrophobic core/hydrophilic shell structured mesoporous silica nanospheres: enhanced adsorption of organic compounds from water.

    Science.gov (United States)

    Li, Shuru; Jiao, Xuan; Yang, Hengquan

    2013-01-29

    Inspired by the structure features of micelle, we attempt to synthesize a novel functionalized mesoporous silica nanosphere consisting of a hydrophobic core and a hydrophilic shell. The obtained solid materials were structurally confirmed by N(2) sorption, X-ray diffraction (XRD), and transmission electron microscopy (TEM). Their compositions were characterized by Fourier transfer infrared spectroscopy (FT-IR), solid state NMR, X-ray photoelectron spectroscopy (XPS), and elemental analysis. Its fundamental properties such as dispersibility in water or organic phase, wettability, and adsorption ability toward hydrophobic organics in water were investigated. It was revealed that these important properties could be facilely adjusted through varying structure and composition. In particular, these materials showed much better adsorption ability toward hydrophobic organic molecules in water than conventional monofunctionalized mesoporous materials, owing to possessing the hydrophobic/hydrophilic domain-segregated and hierarchically functionalized mesoporous structures. The intriguing properties would make mesoporous materials more accessible to many important applications, especially in aqueous systems.

  7. Investigation of Multilayer Organic Insulation Structure on Surface Flashover Properties and Mechanism in Vacuum

    Institute of Scientific and Technical Information of China (English)

    LI Shengtao; HUANG Qifeng

    2013-01-01

    In order to further investigate the surface flashover mechanism in vacuum,the surface flashover and electric field distribution of multilayer organic insulation structure are studied and developed based on the previous studies.The samples ofmultilayer organic insulation structure are prepared by inserting multilayer organic composite material with different relative permittivity between the electrode and the dielectric.Two multilayer organic insulation structures are prepared in this study.One is the cylindrical samples,the other is 45° samples.The impulse (1.2/50 μs) and DC flashover voltages in vacuum are tested,and the electric field distributions of two insulation structures are analyzed by ANSYS.It is found that these two insulation structure could effectively improve the surface flashover performance in vacuum.The results indicate that the highest impulse first flashover voltage of cylindrical samples reaches 65 kV and increases by 25% under impulse voltage.The highest first flashover voltage of/c samples reaches 81 kV and increases by 32% under impulse voltage.The results of electric field simulation demonstrate that different mechanisms exist between 45° insulation structure and cylindrical structure.

  8. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

    Science.gov (United States)

    Song, Na; Chen, Muyan; Gao, Tianxiang; Yanagimoto, Takashi

    2017-01-01

    Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach.

  9. Asymmetric PCR method in generation of HBV ssDNA for pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    Nian-cai Peng; Chun-lin Wang; Li-li Zhang; Mao-li Lu; Zhen-xi Zhang

    2009-01-01

    Objective To explore the optimal primer ratio and concentration of asymmetric polymerase chain reaction (A-PCR) in producing hepatitis B virus (HBV) single-stranded DNA (ssDNA) for pyrosequencing. Methods A-PCR was carried out to generate HBV ssDNA with forward to reverse primers of different ratios (50 : 1, 100 : 1) and concentrations (13. 0 pmol/25μL and 0.14 pmol/25μL, 19. 5 pmol/25μL and 0. 21 pmol/25μL), and the product yield and quality were compared respectively. Results The forward to reverse primer ratio of 50 : 1 provided better yield and concentration of 19. 5 pmol/25μL and 0. 21 pmol//25μL generated a clearer band. Conclusion A simple and feasible method to produce HBV ssDNA for pyrosequencing in batch is established.

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

    DEFF Research Database (Denmark)

    Inceoglu, Özgül; Abu Al-Soud, Waleed; Salles, Joana Falcão

    2011-01-01

    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 stru......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...... 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...

  11. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  12. 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…

  13. [Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing].

    Science.gov (United States)

    Zhao, Yong-Gang; Liu, Hua-Lei; Wang, Jing-Jing; Zheng, Dong-Xia; Zhao, Yun-Ling; Ge, Sheng-Qiang; Wang, Zhi-Liang

    2014-07-01

    This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.

  14. Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis

    OpenAIRE

    2012-01-01

    The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries sugge...

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

    OpenAIRE

    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...

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

    Directory of Open Access Journals (Sweden)

    Svetlana V Shcherbik

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

  17. Self-organization of maze-like structures via guided wrinkling.

    Science.gov (United States)

    Bae, Hyung Jong; Bae, Sangwook; Yoon, Jinsik; Park, Cheolheon; Kim, Kibeom; Kwon, Sunghoon; Park, Wook

    2017-06-01

    Sophisticated three-dimensional (3D) structures found in nature are self-organized by bottom-up natural processes. To artificially construct these complex systems, various bottom-up fabrication methods, designed to transform 2D structures into 3D structures, have been developed as alternatives to conventional top-down lithography processes. We present a different self-organization approach, where we construct microstructures with periodic and ordered, but with random architecture, like mazes. For this purpose, we transformed planar surfaces using wrinkling to directly use randomly generated ridges as maze walls. Highly regular maze structures, consisting of several tessellations with customized designs, were fabricated by precisely controlling wrinkling with the ridge-guiding structure, analogous to the creases in origami. The method presented here could have widespread applications in various material systems with multiple length scales.

  18. Studying the operation characteristics and structure of vertical channel copper-phthalocyanine organic semiconductor transistor

    Institute of Scientific and Technical Information of China (English)

    ZHU Min; SONG Ming-xin; GUI Tai-long; WANG Xuan; YIN Jing-hua; WANG Dong-xing; ZHAO Hong

    2005-01-01

    The creation of Au/CuPc/Al/CuPc/structure is a perpendicular type electricity found in the channel of organic static induction transistor. In the following we analyze transistor operation characteristics and machine structural relation. The results express that the transistor drives the voltage low and has no-saturation currentvoltage characteristics. Its operation characteristics are dependant on gate bias voltage and the construction of the aluminum electrode.The vertical channel of organic static induction transistor (OSIT) , with structure of Au/CuPc/Al/CuPc/Cu, has been determined. According to the test results, the relation of its operation characteristics and device structure was analyzed. The results show that this transistor has a low driving voltage and unsaturation Ⅰ-Ⅴ characteristics. Its operation characteristics are dependant on gate bias voltage and the structure of the aluminum electrode.

  19. Formation of partially ordered organic planar systems based on the in situ control of their structural organization

    Science.gov (United States)

    Dyakova, Yu. A.; Marchenkova, M. A.

    2016-09-01

    The possibilities of significantly improving the quality of planar systems based on photoactive porphyrin-fullerene dyads, layers based on cytochrome c and cardiolipin, and lysozyme crystals and films using a complex of in situ X-ray methods and simulation are described. The potential of X-ray phase-sensitive and surface-sensitive methods developed by M.V. Koval'chuk and researchers from his school in monitoring all stages of synthesis of partially ordered organic structure is demonstrated. This approach shows its efficiency for in situ studies: starting from the formation of complexes in solutions up to the growth of protein films and crystals.

  20. 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.

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

    DEFF Research Database (Denmark)

    Rasmussen, Ole Horn

    of agricultural structural change. We have three different but intertwined treadmills: a product-, land market- and credit treadmill. Our conclusion is that the greatest reason for the first two treadmills is the scarcity of land. The rule of scarcity is a fundamental rule and must be part of any agricultural...... agriculture. The two competing systems of technology operate with different principles. While in principle organic agriculture internalise conventional agriculture seeks to externalise cost into price. Besides, the external economy of conventional agriculture may be larger and create larger economic synergy...... of agricultural structural change. Because organic agriculture is a niche, it is a transformation with an unexploited potential. Whether organic agriculture is a fourth and non-niche transformation is an issue for prediction. The link between transformation and organic agriculture opens up for a theoretical...

  2. 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...

  3. Pyrosequencing for mini-barcoding of fresh and old museum specimens.

    Directory of Open Access Journals (Sweden)

    Shadi Shokralla

    Full Text Available DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53-97 year-old. The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.

  4. 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.

  5. Pyrosequencing for mini-barcoding of fresh and old museum specimens.

    Science.gov (United States)

    Shokralla, Shadi; Zhou, Xin; Janzen, Daniel H; Hallwachs, Winnie; Landry, Jean-François; Jacobus, Luke M; Hajibabaei, Mehrdad

    2011-01-01

    DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53-97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.

  6. Rapid identification of strains belonging to the Mycobacterium abscessus group through erm(41) gene pyrosequencing.

    Science.gov (United States)

    Yoshida, Shiomi; Tsuyuguchi, Kazunari; Suzuki, Katsuhiro; Tomita, Motohisa; Okada, Masaji; Shimada, Ryoko; Hayashi, Seiji

    2014-07-01

    Mycobacterium abscessus and Mycobacterium massiliense lung infections have different clarithromycin susceptibilities, making proper identification important; however, standard multi-gene sequencing in clinical laboratories is laborious and time consuming. We developed a pyrosequencing-based method for rapid identification of strains belonging to the M. abscessus group by targeting erm(41). We examined 55 isolates from new pulmonary M. abscessus infections and identified 28 M. abscessus, 25 M. massiliense, and 2 Mycobacterium bolletii isolates. Multi-gene sequencing of 16S rRNA, hsp65, rpoB, and the 16S-23S ITS region was concordant with the results of erm(41) pyrosequencing; thus, the M. abscessus group can be identified by single-nucleotide polymorphisms in erm(41). The method also enables rapid identification of polymorphic, inducible clarithromycin-resistant sequevars (T28 or C28). Pyrosequencing of erm(41) is a rapid, reliable, high-throughput alternative method for identifying and characterizing M. abscessus species. Further testing of a diverse collection of isolates is necessary to demonstrate the discriminatory power of erm(41) sequencing to differentiating species with this highly divergent group.

  7. 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.

  8. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer.

    Science.gov (United States)

    Wang, Gary P; Garrigue, Alexandrine; Ciuffi, Angela; Ronen, Keshet; Leipzig, Jeremy; Berry, Charles; Lagresle-Peyrou, Chantal; Benjelloun, Fatine; Hacein-Bey-Abina, Salima; Fischer, Alain; Cavazzana-Calvo, Marina; Bushman, Frederic D

    2008-05-01

    Gene transfer has been used to correct inherited immunodeficiencies, but in several patients integration of therapeutic retroviral vectors activated proto-oncogenes and caused leukemia. Here, we describe improved methods for characterizing integration site populations from gene transfer studies using DNA bar coding and pyrosequencing. We characterized 160,232 integration site sequences in 28 tissue samples from eight mice, where Rag1 or Artemis deficiencies were corrected by introducing the missing gene with gamma-retroviral or lentiviral vectors. The integration sites were characterized for their genomic distributions, including proximity to proto-oncogenes. Several mice harbored abnormal lymphoproliferations following therapy--in these cases, comparison of the location and frequency of isolation of integration sites across multiple tissues helped clarify the contribution of specific proviruses to the adverse events. We also took advantage of the large number of pyrosequencing reads to show that recovery of integration sites can be highly biased by the use of restriction enzyme cleavage of genomic DNA, which is a limitation in all widely used methods, but describe improved approaches that take advantage of the power of pyrosequencing to overcome this problem. The methods described here should allow integration site populations from human gene therapy to be deeply characterized with spatial and temporal resolution.

  9. 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

  10. 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

    2017-09-26

    Graphene (GN) and graphene oxides (GOs) are novel carbon nanomaterial, they have been attracted much attention because of their excellent properties and are widely applied in many areas including energy, electronics, biomedicine and environmental science etc. With industrial production and consumption of GN/GO, they will inevitably enter the soil and water environment. GN/GO may directly cause certain harm to microorganisms and lead to ecological and environmental risks. Graphene oxides are graphene derivative with abundant oxygen-containing functional groups in its graphitic backbone. The structure and chemistry of graphene show obvious differences compared with graphene oxide, which lead to the different environmental behaviors. In this study, four different types of soil (S1, S2, S3 and 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, actinomycete and fungi) changed after GN/GO release into soils. Soil microbial community species are more richness and the diversity also increase 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 applying at 90 DAT in S1 and reached 4.6%. Proteobacteria were the most phylum in S2, S3 and S4 soils, it ranged from 43.6% to 71.4% in S2, 45.6% to 73.7% in S3, 38.1% to 56.7% in S4, respectively. The most abundant genus were Bacillus (37.5% - 47.0%), Lactococcus (28.0% - 39.0%) in S1, Lysobacter and Flavobacterium in S2, Pedobacter in S3 and Massilia in S4 soil. The effect of GN and GO on soil microbial community is time dependent, and there are no significant differences between the samples at 10 and 90 DAT.

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, Lucia; Caillard, Renaud; MartIn-Gago, Jose A; Mendez, Javier [Grupo ESISNA, Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Cientificas (CSIC), c/ Sor Juana Ines de la Cruz 3, Campus de Cantoblanco, E-28049 Madrid (Spain); Pelaez, Samuel; Serena, Pedro A, E-mail: jmendez@icmm.csic.es [Grupo de Teoria y Simulacion de Materiales, Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Cientificas (CSIC), c/ Sor Juana Ines de la Cruz 3, Campus de Cantoblanco, E-28049 Madrid (Spain)

    2010-07-30

    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.

  13. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    Science.gov (United States)

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport.

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

    Science.gov (United States)

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

    2016-03-01

    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.

  15. An Investigation on a Production Company via the Scope of Mintzberg’s Adhocratic Organization Structure

    Directory of Open Access Journals (Sweden)

    Yasin Cakirel

    2016-01-01

    Full Text Available Today, the importance of innovation for enterprises, increase each passing day. As a result of globalization, enterprises are under intense competitive pressure. They have to make innovation for increasing to market share or for protecting to it at least. Noninnovative firms lose their customers and their existence is face to threat from other innovative actors in the market. Therefore firms have to design their organization structure that encourage to innovation. Mintzberg’s adhocratic organization structure was investigated in this article. Thus, its aim of this study leads to resemblance and diversity between theory and practice via of the theoretical knowledge. As a result of study; high degree of similarity between the application and Mintzberg’s theory, which is related to adhocratic organization structure, has been identified.

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

    Directory of Open Access Journals (Sweden)

    Carlos Sáenz-Royo

    Full Text Available 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.

  17. 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

  18. 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.

    2017-01-01

    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, 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. PMID:28198425

  19. Investigation of organic films by atomic force microscopy: Structural, nanotribological and electrical properties

    Science.gov (United States)

    Qi, Yabing

    2011-11-01

    Atomic force microscopy (AFM) has found its applications in a wide range of research fields. In this review, we show by examples that atomic force microscopy is a powerful technique to investigate structural, mechanical and electrical properties of organic films. We start with an introduction of AFM instrumentation highlighting AFM developments that are of direct relevance to organic films. Next, we review AFM studies on organic films according to their preparation methods: self-assembly, the Langmuir-Blodgett technique, solution preparation, and thermal evaporation. In the discussion on self-assembled monolayers, we focus on aspects such as structural evolution, load-induced molecular tilting, annealing, and incorporation of conjugated groups. For solution prepared organic films, we stress annealing-induced structural evolution as well as the effects of phase separation/segregation. We also briefly summarize the progress of AFM investigation on Langmuir-Blodgett films and thermally evaporated organic films. We conclude the review by providing some thoughts for future exploration. In particular, atomic force microscopy combined with ultra-flat coplanar nano-electrodes provides a promising platform to isolate single or a small number of molecular features (e.g. vacancies, defects, grain boundaries) in organic films as well as to identify the role of these features at the nanometer scale.

  20. 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.

  1. Organic content influences sediment microbial fuel cell performance and community structure.

    Science.gov (United States)

    Zhao, Qing; Li, Ruying; Ji, Min; Ren, Zhiyong Jason

    2016-11-01

    This study constructed sediment microbial fuel cells (SMFCs) with different organic loadings without the amendment of external substrates, and it investigated how such variation affects electricity generation and microbial community structure. Results found sediment characteristics significantly influenced SMFC performance and appropriate organic content is important to maintain stable power outputs. SMFCs with loss of ignition (LOI) of 5% showed the most reliable performance in this study, while high organic content (LOI 10-16%) led to higher but very unstable voltage output because of biogas accumulation and worm activities. SMFCs with low organic content (1-3%) showed low power output. Different bacterial communities were found in SMFCs shown various power generation performance even those with similar organic contents. Thermodesulfovibrionaceae was found closely related to the system startup and Desulfobulbaceae showed great abundance in SMFCs with high power production.

  2. Pyrosequencing-based analysis reveals a novel capsular gene cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil

    Directory of Open Access Journals (Sweden)

    Ramos Pablo Ivan

    2012-08-01

    Full Text Available Abstract Background An important virulence factor of Klebsiella pneumoniae is the production of capsular polysaccharide (CPS, a thick mucus layer that allows for evasion of the host's defense and creates a barrier against antibacterial peptides. CPS production is driven mostly by the expression of genes located in a locus called cps, and the resulting structure is used to distinguish between different serotypes (K types. In this study, we report the unique genetic organization of the cps cluster from K. pneumoniae Kp13, a clinical isolate recovered during a large outbreak of nosocomial infections that occurred in a Brazilian teaching hospital. Results A pyrosequencing-based approach showed that the cps region of Kp13 (cpsKp13 is 26.4 kbp in length and contains genes common, although not universal, to other strains, such as the rmlBADC operon that codes for L-rhamnose synthesis. cpsKp13 also presents some unique features, like the inversion of the wzy gene and a unique repertoire of glycosyltransferases. In silico comparison of cpsKp13 RFLP pattern with 102 previously published cps PCR-RFLP patterns showed that cpsKp13 is distinct from the C patterns of all other K serotypes. Furthermore, in vitro serotyping showed only a weak reaction with capsular types K9 and K34. We confirm that K9 cps shares common genes with cpsKp13 such as the rmlBADC operon, but lacks features like uge and Kp13-specific glycosyltransferases, while K34 capsules contain three of the five sugars that potentially form the Kp13 CPS. Conclusions We report the first description of a cps cluster from a Brazilian clinical isolate of a KPC-producing K. pneumoniae. The gathered data including K-serotyping support that Kp13’s K-antigen belongs to a novel capsular serotype. The CPS of Kp13 probably includes L-rhamnose and D-galacturonate in its structure, among other residues. Because genes involved in L-rhamnose biosynthesis are absent in humans, this pathway may represent

  3. The small-world organization of large-scale brain systems and relationships with subcortical structures.

    Science.gov (United States)

    Koziol, Leonard F; Barker, Lauren A; Joyce, Arthur W; Hrin, Skip

    2014-01-01

    Brain structure and function is characterized by large-scale brain systems. However, each system has its own "small-world" organization, with sub-regions, or "hubs," that have varying degrees of specialization for certain cognitive and behavioral processes. This article describes this small-world organization, and the concepts of functional specialization and functional integration are defined and explained through practical examples. We also describe the development of large-scale brain systems and this small-world organization as a sensitive, protracted process, vulnerable to a variety of influences that generate neurodevelopmental disorders.

  4. 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.

  5. Preparation and applications of monolithic structures containing metal-organic frameworks.

    Science.gov (United States)

    Lv, Yongqin; Tan, Xinyi; Svec, Frantisek

    2017-01-01

    Metal-organic frameworks are a new category of advanced porous materials with large surface areas and porosities, uniform pore sizes, tunable surface chemistry, and structural diversity. In combination with monoliths, they allow the fine tuning of desired interactions required in a variety of applications. This review article summarizes results of recent studies focused on synthetic strategies enabling incorporation of metal-organic frameworks in monolithic structures. A diverse array of applications including chromatographic separation, solid-phase microextraction, sample enrichment, heterogeneous catalysis, and enzymatic catalysis are also described. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Implementation of submicrometric periodic surface structures toward improvement of organic-solar-cell performances

    Science.gov (United States)

    Cocoyer, C.; Rocha, L.; Sicot, L.; Geffroy, B.; de Bettignies, R.; Sentein, C.; Fiorini-Debuisschert, C.; Raimond, P.

    2006-03-01

    Submicrometric periodic patterning of an organic solar cell surface is investigated in order to optimize the photovoltaic conversion efficiency of the device. Patterning is achieved using a single-step all-optical technique based on photoinduced mass transport in azopolymer films. The polymer film with a structured surface is used as a substrate for an organic solar cell based on a copper phthalocyanine/C60 heterojunction. The effect of periodic patterning is investigated through the solar-cell optical-absorption properties and external quantum efficiency measurements. The possibility to increase the short circuit current density and the corresponding photovoltaic conversion efficiency is evidenced with one-dimensional periodic structures.

  7. Structure and function of an inorganic-organic separator for electrochemical cells: Preliminary study

    Science.gov (United States)

    Bozek, J. M.

    1974-01-01

    The structure of a new separator material for electrochemical cells has been investigated. Investigation into details of the separator structure showed it to be multilayered and to consist mainly of a quasi-impervious organic skin, a porous region of mixed organic and inorganic material, and an area of nonuniformly treated substrate. The essential feature of the coating (slurry) is believed to be interconnected pores which allow ionic conductivity. The interconnected pores are believed to be formed by the interaction of the plasticizer and inorganic fibers. The major failure mode of silver zinc cells using such a separator (zinc nodules shorting adjacent plates) was investigated.

  8. X-ray method for the structural investigation of thin organic films

    Energy Technology Data Exchange (ETDEWEB)

    Rieutord, F.; Benattar, J.J.; Bosio, L.

    1986-07-01

    The structures of thin lamellar films can be determined through a combination of three X-ray experiments using synchrotron radiation. Diffraction experiments in the transmission geometry give the intralamellar ordering, the diffraction at small glancing angles yields the interlamellar organization, and the critical reflection provides the density measurement which is required to obtain the number of structural units per cell. This method is illustrated here with the study of an organic compound deposited in Langmuir-Blodgett films. The compound under study is the complex (N-docosylpyridinium, tetracyano-quino-dimethane TCNQ).

  9. A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies.

    Science.gov (United States)

    Hoppe, Björn; Krger, Krüger; Kahl, Tiemo; Arnstadt, Tobias; Buscot, François; Bauhus, Jürgen; Wubet, Tesfaye

    2015-04-08

    Deadwood is an important biodiversity hotspot in forest ecosystems. While saproxylic insects and wood-inhabiting fungi have been studied extensively, little is known about deadwood-inhabiting bacteria. The study we present is among the first to compare bacterial diversity and community structure of deadwood under field conditions. We therefore compared deadwood logs of two temperate forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing to identify changes in bacterial diversity and community structure at different stages of decay in forest plots under different management regimes. Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic groups in both tree species. There were no differences in bacterial OTU richness between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order Rhizobiales became more abundant during the intermediate and advanced stages of decay, accounting for up to 25% of the entire bacterial community in such logs. The most dominant OTU was taxonomically assigned to the genus Methylovirgula, which was recently described in a woodblock experiment of Fagus sylvatica. Besides tree species we were able to demonstrate that deadwood physico-chemical properties, in particular remaining mass, relative wood moisture, pH, and C/N ratio serve as drivers of community composition of deadwood-inhabiting bacteria.

  10. Pyrosequencing reveals bacterial community differences in composting and vermicomposting on the stabilization of mixed sewage sludge and cattle dung.

    Science.gov (United States)

    Lv, Baoyi; Xing, Meiyan; Yang, Jian; Zhang, Liangbo

    2015-12-01

    This study aimed to compare the microbial community structures and compositions in composting and vermicomposting processes. We applied 454 high-throughput pyrosequencing to analyze the 16S rRNA gene of bacteria obtained from bio-stabilization of sewage sludge and cattle dung. Results demonstrated that vermicomposting process presented higher operational taxonomic units and bacterial diversity than the composting. Analysis using weighted UniFrac indicated that composting exhibited higher effects on shaping microbial community structure than the vermicomposting. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting and shifted to Actinomycetes in the maturing stage. By contrast, Proteobacteria accounted for the highest proportions in the whole process of the vermicomposting. Furthermore, vermicomposting contained more uncultured and unidentified bacteria at the taxonomy level of genus than the composting. In summary, the bacterial community during composting significantly differed from that during vermicomposting. These two techniques played different roles in changing the diversity and composition of microbial communities.

  11. 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.

  12. 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.

  13. 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, sport participation that was partially mediated by perceived family wealth.

  14. Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome.

    Directory of Open Access Journals (Sweden)

    Melody S Clark

    Full Text Available BACKGROUND: The Antarctic krill Euphausia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. Hence, understanding how this organism functions is a priority area and will provide fundamental data for life history studies, energy budget calculations and food web models. METHODOLOGY/PRINCIPAL FINDINGS: The assembly of the 454 transcriptome of E. superba resulted in 22,177 contigs with an average size of 492bp (ranging between 137 and 8515bp. In depth analysis of the data revealed an extensive catalogue of the cellular chaperone systems and the major antioxidant proteins. Full length sequences were characterised for the chaperones HSP70, HSP90 and the super-oxide dismutase antioxidants, with the discovery of potentially novel duplications of these genes. The sequence data contained 41,470 microsatellites and 17,776 Single Nucleotide Polymorphisms (SNPs/INDELS, providing a resource for population and also gene function studies. CONCLUSIONS: This paper details the first 454 generated data for a pelagic Antarctic species or any pelagic crustacean globally. The classical "stress proteins", such as HSP70, HSP90, ferritin and GST were all highly expressed. These genes were shown to be over expressed in the transcriptomes of Antarctic notothenioid fish and hypothesized as adaptations to living in the cold, with the associated problems of decreased protein folding efficiency and increased vulnerability to damage by reactive oxygen species. Hence, these data will provide a major resource for future physiological work on krill, but in particular a suite of "stress" genes for studies understanding

  15. Assessment of tillage systems in organic farming: influence of soil structure on microbial biomass. First results

    OpenAIRE

    Vian, Jean François; Peigné, Joséphine; Chaussod, Rémi; Roger-Estrade, Jean

    2007-01-01

    Soil tillage modifies environmental conditions of soil microorganisms and their ability to release nitrogen. We compare the influence of reduced tillage (RT) and mouldboard ploughing (MP) on the soil microbial functioning in organic farming. In order to connect soil structure generated by these tillage systems on the soil microbial biomass we adopt a particular sampling scheme based on the morphological characterisation of the soil structure by the description of the soil profile. This method...

  16. Electrochemical properties of honeycomb-like structured HFBI self-organized membranes on HOPG electrodes.

    Science.gov (United States)

    Yamasaki, Ryota; Takatsuji, Yoshiyuki; Lienemann, Michael; Asakawa, Hitoshi; Fukuma, Takeshi; Linder, Markus; Haruyama, Tetsuya

    2014-11-01

    HFBI (derived from Trichoderma sp.) is a unique structural protein, which forms a self-organized monolayer at both air/water interface and water/solid interfaces in accurate two-dimensional ordered structures. We have taken advantage of the unique functionality of HFBI as a molecular carrier for preparation of ordered molecular phase on solid substrate surfaces. The HFBI molecular carrier can easily form ordered structures; however, the dense molecular layers form an electrochemical barrier between the electrode and solution phase. In this study, the electrochemical properties of HFBI self-organized membrane-covered electrodes were investigated. Wild-type HFBI has balanced positive and negative charges on its surface. Highly oriented pyrolytic graphite (HOPG) electrodes coated with HFBI molecules were investigated electrochemically. To improve the electrochemical properties of this HFBI-coated electrode, the two types of HFBI variants, with oppositely charged surfaces, were prepared genetically. All three types of HFBI-coated HOPG electrode perform electron transfer between the electrode and solution phase through the dense HFBI molecular layer. This is because the HFBI self-organized membrane has a honeycomb-like structure, with penetrating holes. In the cases of HFBI variants, the oppositely charged HFBI membrane phases shown opposite electrochemical behaviors in electrochemical impedance spectroscopy. HFBI is a molecule with a unique structure, and can easily form honeycomb-like structures on solid material surfaces such as electrodes. The molecular membrane phase can be used for electrochemical molecular interfaces.

  17. [Effects of nitrate on organic removal and microbial community structure in the sediments].

    Science.gov (United States)

    Liu, Jin; Deng, Dai-Yong; Sun, Guo-Ping; Liu, Yong-Ding; Xu, Mei-Ying

    2013-07-01

    The strategy promoted pollutant degradation and transformation under the anaerobic circumstance by adding nitrate as an electron acceptor has been widely used in sediment bioremediation. However, few literature reports on organic removal characteristics and microbial community responses in the contaminated river sediment under the nitrate reduction condition. Methods including the polar and non-polar chemical fractionation, relative abundance detection of organic matters by GC-MS were combined and applied to investigate organic removals and PCR-DGGE analysis was used for microbial community structures in sediment incubation systems with or without calcium nitrate addition. The results indicated that the addition of calcium nitrate could significantly enhance removal efficiencies of organic pollutants. The removal efficiency of total organic carbon (TOC) and the total peak area of organic matters in GC-MS were 47.25% and 29.55% which were higher than those of the control. The effect descending order of organic pollutants was: silicon materials > alkanes > polycyclic aromatic hydrocarbons > heterocyclic compounds > olefins > benzene homologues > polar compounds > phthalates > aldehydes and ketones > alkyl esters. And removal rates of silicon materials, the persistent organic pollutants, benzene homologues and heterocyclic compounds were 46.73%, 36.25%, 23.19% and 35.92% which were higher than those of the control. The PCR-DGGE profile of bacterial 16S rDNA V3 fragments showed obviously different microbial community structures between the treatment and the control systems. Blastn analysis revealed that sequences of 10 predominant bands from DGGE profile were closely related to Proteobacteria, Actinobacteria, Clostridia, Chloroflexi, Caldiserica and uncultured bacterium. The research findings provide some helpful scientific information for promoting organic pollutant removal of river sediment by nitrate reduction.

  18. Pyrosequencing analysis of the bacterial community in drinking water wells.

    Science.gov (United States)

    Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

    2013-07-01

    Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

  19. The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview.

    Science.gov (United States)

    Costantini, Maria; Musto, Héctor

    2017-03-01

    The recent availability of a number of fully sequenced genomes (including marine organisms) allowed to map very precisely the isochores, based on DNA sequences, confirming the results obtained before genome sequencing by the ultracentrifugation in CsCl. In fact, the analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong to a small number of families characterized by different GC levels. In this review, we will concentrate on some general genome features regarding the compositional organization from different organisms and their evolution, ranging from vertebrates to invertebrates until unicellular organisms. Since isochores are tightly linked to biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function, and evolution. All the findings reported here confirm the idea that the isochores can be considered as a "fundamental level of genome structure and organization." We stress that we do not discuss in this review the origin of isochores, which is still a matter of controversy, but we focus on well established structural and physiological aspects.

  20. Macrozoobenthic community structure in two Portuguese estuaries: Relationship with organic enrichment and nutrient gradients

    Science.gov (United States)

    Mucha, Ana Paula; Costa, Maria Helena

    1999-07-01

    The aim of this work consists in the study of the structural and functional aspects of the macrozoobenthic communities and their relationships with the organic enrichment and nutrient gradients in water and sediment. The study was carried out in two coastal ecosystems under strong anthropogenic pressure: the Sado estuary and the Aveiro Lagoon. Samples were collected at four stations between October 1994 and April 1995. The results obtained allowed us to state that spatial variability, both horizontal and vertical, was higher than the temporal variability. This was due to local hydrodynamism, organic load and granulometric structure of the sediment. Comparing the community structure at the different stations, it was possible to observe the existence of disturbance cases not directly related to organic enrichment gradients. The interpretation of the functional role of the macrozoobenthic communities at the water-sediment interface was based on the trophodynamic group classification. This approach allowed us to state that the sensitivity of different groups to organic enrichment, confirming the role of burrower subsurface-deposit feeders as opportunists associated with organic enrichment and, on the other hand, the influence of certain trophodynamic groups in the nutrient transfer processes, particularly the association between tube-builder omnivores and burrower carnivore and nitrate content in interstitial water.

  1. Water Dynamics and Its Role in Structural Hysteresis of Dissolved Organic Matter.

    Science.gov (United States)

    Conte, Pellegrino; Kucerik, Jiri

    2016-03-01

    Knowledge of structural dynamics of dissolved organic matter (DOM) is of paramount importance for understanding DOM stability and role in the fate of solubilized organic and inorganic compounds (e.g., nutrients and pollutants), either in soils or aquatic systems. In this study, fast field cycling (FFC) (1)H NMR relaxometry was applied to elucidate structural dynamics of terrestrial DOM, represented by two structurally contrasting DOM models such as Suwanee River (SRFA) and Pahokee peat (PPFA) fulvic acids purchased by the International Humic Substance Society. Measurement of NMR relaxation rate of water protons in heating-cooling cycles revealed structural hysteresis in both fulvic acids. In particular, structural hysteresis was related to the delay in re-establishing water network around fulvic molecules as a result of temperature fluctuations. The experiments revealed that the structural temperature dependency and hysteresis were more pronounced in SRFA than in PPFA. This was attributed to the larger content of hydrogel-like structure in SRFA stabilized, at a larger extent, by H-bonds between carboxylic and phenolic groups. Moreover, results supported the view that terrestrial DOM consist of a hydrophobic rigid core surrounded by progressively assembling amphiphilic and polar molecules, which form an elastic structure that can mediate reactivity of the whole DOM.

  2. 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.

  3. Organization of the 2013 Structured Light in Structured Media: From Classical to Quantum Optics Incubator

    Science.gov (United States)

    2015-08-02

    metamaterials made on optical fiber platform. These studies resulted in the following main findings: i) Magnetic metamaterials can be used to manipulate...open to new exciting ideas in other fields. Her current research interests are nanoscale magnetic systems and plasmonic metamaterials . Natalia...light”), optical metamaterials (“structured media”), and potential applications for quantum optics and single photon interactions. Understanding the

  4. Modeling the influence of alkane molecular structure on secondary organic aerosol formation.

    Science.gov (United States)

    Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha

    2013-01-01

    Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors.

  5. Fine structure of uterus and non-functioning paruterine organ in Orthoskrjabinia junlanae (Cestoda, Cyclophyllidea).

    Science.gov (United States)

    Korneva, Janetta V; Kornienko, Svetlana A; Jones, Malcolm K

    2016-06-01

    Some cyclophyllidean cestodes provide protection for their eggs in the external environment by providing them with additional protective layers around the egg membranes. In attempting to examine such adaptations, the microanatomy and fine structure of the uterus of pregravid and gravid proglottids of the cyclophyllidean cestode Orthoskrjabinia junlanae, a parasite of mammals that inhabit a terrestrial but moist environment, were studied. In the initial stages of uterine development, developing embryos locate freely in the lumen of a saccate uterus that later partitions into chambers. Each chamber that forms encloses several embryos. The chambers are surrounded by muscle cells that synthesize extracellular matrix actively. The paruterine organs consist of stacks of flattened long outgrowths of muscular cells, interspersed with small lipid droplets. In the gravid proglottids, the size of paruterine organ increases and consists of flattened basal and small rounded apical parts separated by constrictions. The fine structure of the organ wall remains the same: sparse nuclei and stacks of flattened cytoplasmic outgrowths but internal invaginations or lumen in the paruterine organ are absent. Completely developed eggs remain localized in the uterus. Based on the comparative morpho-functional analysis of uterine and paruterine organs and uterine capsules in cestodes, we conclude that these non-functioning paruterine organ in O. junlanae is an example of an atavism. We postulate that the life cycle of the parasite, which infects mammals living in wet habitats, where threats of desiccation of parasite ova is reduced, has favoured a reversion to a more ancestral form of uterine development.

  6. Teaching Basic Science Environmentally, The Concept: The cell is basic unit of structure of most organisms.

    Science.gov (United States)

    Busch, Phyllis S.

    1985-01-01

    Suggests simple ways to introduce students to the concept that the cell is the basic unit of structure of most organisms. Mentions materials for microscope study that are readily available and easy to handle, e.g., membranes from between the scales of the onion bulb, thin-leaved plants, pond water, and pollen. (JHZ)

  7. A Conceptual Framework of Corporate and Business Ethics across Organizations: Structures, Processes and Performance

    Science.gov (United States)

    Svensson, Goran; Wood, Greg

    2011-01-01

    Purpose: The objective of this paper is to introduce and describe a conceptual framework of corporate and business ethics across organizations in terms of ethical structures, ethical processes and ethical performance. Design/methodology/approach: A framework is outlined and positioned incorporating an ethical frame of reference in the field of…

  8. 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...

  9. Method for analyzing structural changes of flexible metal-organic frameworks induced by adsorbates

    NARCIS (Netherlands)

    Dubbeldam, D.; Krishna, R.; Snurr, R.Q.

    2009-01-01

    Metal−organic frameworks (MOFs) have crystal structures that exhibit unusual flexibility. An extreme example is that of the "breathing MOF" MIL-53 that expands or shrinks to admit guest molecules like CO2 and water. We present a powerful simulation tool to quickly calculate unit cell shape and size

  10. Metal-Organic Frameworks with d-f Cyanide Bridges: Structural Diversity, Bonding Regime, and Magnetism

    NARCIS (Netherlands)

    Ferbinteanu, M.; Cimpoesu, F.; Tanase, S.; Cheng, P.

    2015-01-01

    We present a selection of metal-organic frameworks based on d-f and f-f linkages, discussing their structural features and properties from experimental and theoretical viewpoints. We give an overview of our own synthetic and modeling methodologies, highlighting the complexity of the

  11. Covalent organic frameworks with spatially confined guest molecules in nanochannels and their impacts on crystalline structures.

    Science.gov (United States)

    Gao, Jia; Jiang, Donglin

    2016-01-25

    We demonstrate the profound effects of spatially confined guest molecules in one-dimensional nanochannels on X-ray diffraction behaviors of covalent organic frameworks. Our results give insights into the abnormal X-ray diffraction patterns and suggest a novel molecular dynamic strategy for resolving crystalline structures.

  12. Material structure-composite morphology-photovoltaic performance relationship for organic bulk heterojunction solar cells.

    Science.gov (United States)

    Troshin, Pavel A; Mukhacheva, Olga A; Goryachev, Andrey E; Dremova, Nadezhda N; Voylov, Dmitry; Ulbricht, Christoph; Egbe, Daniel A M; Sariciftci, Niyazi Serdar; Razumov, Vladimir F

    2012-10-01

    Conjugated PPV-PPE copolymer has been investigated in organic solar cells in combination with twelve different fullerene derivatives. It was shown that the length of solubilizing alkyl chains in the fullerene derivative structures correlates well with the performance of photovoltaic cells.

  13. Ethnically Diverse Students' Knowledge Structures in First-Semester Organic Chemistry

    Science.gov (United States)

    Lopez, Enrique J.; Shavelson, Richard J.; Nandagopal, Kiruthiga; Szu, Evan; Penn, John

    2014-01-01

    Chemistry courses remain a challenge for many undergraduate students. In particular, first-semester organic chemistry has been labeled as a gatekeeper with high attrition rates, especially among students of color. Our study examines a key factor related to conceptual understanding in science and predictive of course outcomes-knowledge structures.…

  14. Structure of hybrid organic-inorganic sols for the preparation of hydrothermally stable membranes

    NARCIS (Netherlands)

    Castricum, H.L.; Sah, A.; Geenevasen, J.A.J.; Kreiter, R.; Blank, D.H.A.; Vente, J.F.; ten Elshof, J.E.

    2008-01-01

    A procedure for the preparation of hybrid sols for the synthesis of organic-inorganic microporous materials and thin film membranes is reported. We describe silane reactivity and sol structure for acid-catalysed colloidal sols from mixtures of either tetraethylorthosilicate (TEOS) and methyltriethox

  15. Method for analyzing structural changes of flexible metal-organic frameworks induced by adsorbates

    NARCIS (Netherlands)

    Dubbeldam, D.; Krishna, R.; Snurr, R.Q.

    2009-01-01

    Metal−organic frameworks (MOFs) have crystal structures that exhibit unusual flexibility. An extreme example is that of the "breathing MOF" MIL-53 that expands or shrinks to admit guest molecules like CO2 and water. We present a powerful simulation tool to quickly calculate unit cell shape and size

  16. 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.

  17. 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...

  18. Modeling the Self-Assembly of Organic Molecules in 2D Molecular Layers with Different Structures

    NARCIS (Netherlands)

    van der Lit, J.; Marsman, J.L.; Koster, R.S.; Jacobse, Peter; den Hartog, Stephan; Vanmaekelbergh, Daniel; Klein Gebbink, Bert; Filion, Laura; Swart, Ingmar

    2016-01-01

    If organic molecules are to be used as the active component in devices, self-assembly represents the most attractive route to control the geometric structure and therefore part of the device performance. High-resolution scanning tunneling microscopy measurement combined with density functional theor

  19. Structure of phase-separated ferroelectric/ semiconducting polymer blends for organic non-volatile memories

    NARCIS (Netherlands)

    Mcneill, C.R.; Asadi, K.; Watts, B.; Blom, P.W.M.; Leeuw, D.M. de

    2010-01-01

    The phase-separated structure of blends of the ferroelectric polymer P(VDF-TrFE) and the semiconducting polymer P3HT used in organic non-volatile memories is revealed with soft X-ray spectromicroscopy. These thin-film blends show a columnar morphology, with P3HT-rich columns enclosed in a continuous

  20. Preparation of Ferrierite Zeolite Membranes in the Absence of Organic Structure-directing Agents

    Institute of Scientific and Technical Information of China (English)

    Xiao Hui SU; Gang LI; Rui Sen LIN; Eiichi KIKUCHI; Masahiko MATSUKATA

    2006-01-01

    Ferrierite zeolite membranes were prepared for the first time in the absence of organic structure-directing agents (SDA) on the surface of a porous α-alumina support. These membranes were characterized by means of X-ray diffraction (XRD), scanning electron microscopy (SEM) and pervaporation tests.

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

    Science.gov (United States)

    Kelley, Steven P.; Rogers, Robin D.

    2017-01-01

    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. PMID:28875025

  2. 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.

  3. A Conceptual Framework of Corporate and Business Ethics across Organizations: Structures, Processes and Performance

    Science.gov (United States)

    Svensson, Goran; Wood, Greg

    2011-01-01

    Purpose: The objective of this paper is to introduce and describe a conceptual framework of corporate and business ethics across organizations in terms of ethical structures, ethical processes and ethical performance. Design/methodology/approach: A framework is outlined and positioned incorporating an ethical frame of reference in the field of…

  4. Modeling structure and flexibility of Candida antarctica lipase B in organic solvents

    Directory of Open Access Journals (Sweden)

    Pleiss Jürgen

    2008-02-01

    Full Text Available Abstract Background The structure and flexibility of Candida antarctica lipase B in water and five different organic solvent models was investigated using multiple molecular dynamics simulations to describe the effect of solvents on structure and dynamics. Interactions of the solvents with the protein and the distribution of water molecules at the protein surface were examined. Results The simulated structure was independent of the solvent, and had a low deviation from the crystal structure. However, the hydrophilic surface of CALB in non-polar solvents decreased by 10% in comparison to water, while the hydrophobic surface is slightly increased by 1%. There is a large influence on the flexibility depending on the dielectric constant of the solvent, with a high flexibility in water and a low flexibility in organic solvents. With decreasing dielectric constant, the number of surface bound water molecules significantly increased and a spanning water network with an increasing size was formed. Conclusion The reduced flexibility of Candida antarctica lipase B in organic solvents is caused by a spanning water network resulting from less mobile and slowly exchanging water molecules at the protein-surface. The reduced flexibility of Candida antarctica lipase B in organic solvent is not only caused by the interactions between solvent-protein, but mainly by the formation of a spanning water network.

  5. Metal-Organic Frameworks with d-f Cyanide Bridges: Structural Diversity, Bonding Regime, and Magnetism

    NARCIS (Netherlands)

    M. Ferbinteanu; F. Cimpoesu; S. Tanase

    2015-01-01

    We present a selection of metal-organic frameworks based on d-f and f-f linkages, discussing their structural features and properties from experimental and theoretical viewpoints. We give an overview of our own synthetic and modeling methodologies, highlighting the complexity of the interdisciplinar

  6. 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

  7. TERRITORIAL STRUCTURES AND THE POTENTIAL OF ROMANIA’S ORGANIC AGRICULTURAL HOLDINGS

    Directory of Open Access Journals (Sweden)

    Iulian ALECU

    2015-04-01

    Full Text Available The paper seeks to highlight the main issues that the implementation of organic agriculture in Romania has to face, at territorial and national level in regard to the situation of the vegetal and animal sector. The comparison of the percentages showed, on the one hand, a considerable organic potential at national level, and on the other hand, the necessity to embrace a different structure by means of organizational measures. The level of the used markers highlighted an increasing trend of organic agriculture, by means of the increase of the total area and of the areas in conversion. This can be achieved by increasing the average surface per holding and intensifying the average number of animals per organic agricultural holding, situations which at present, at national level, are associated with very noticeable variation forms.

  8. Performance Evaluation of Rural Cooperative Economic Organizations in Hunan Province Based on Structural Equation

    Institute of Scientific and Technical Information of China (English)

    Naman; YANG

    2015-01-01

    Using the method of structural equation and balanced scorecard,this paper establishes the evaluation indicators and evaluation model for the performance of 21 rural cooperative economic organizations in X City of Hunan Province,and analyzes the relationship between indicators and dimensions of performance evaluation indicators,in order to find the influencing factors,obstacles and successful experience concerning the development of rural cooperative economic organizations. According to model analysis and conclusions,this paper sets forth the recommendations for promoting the development of rural cooperative economic organizations in Hunan Province,in order to provide a scientific basis for the institutional design and mechanism innovation of rural cooperative economic organizations in Hunan Province.

  9. Estimation of Formation Enthalpies of Organic Pollutants from a New Structural Group Contribution Method

    Institute of Scientific and Technical Information of China (English)

    Mehdi Bagheri; Afshin Bakhtiari; Masoume Jaberi

    2013-01-01

    Chemical stability and reactivity of organic pollutants is dependent to their formation enthalpies.The main objective of this study is to provide simple straightforward strategy for prediction of the formation enthalpies of wide range organic pollutants only from their structural functional groups.Using such an extended dataset comprising 1694 organic chemicals from 77 diverse material classes benefits the generalizability and reliability of the study.The new suggested collection of 12 functional groups and a simple linear regression lead to promising statistics of R2=0.958,Q2Loo =0.956,and δAEE=57 kJ·mol-1 for the whole dataset.Moreover,unknown experimental formation enthalpies for 27 organic pollutants are estimated by the presented approach.The resultant model needs no technical software/calculations,and thus can be easily applied by a non-specialist user.

  10. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    Science.gov (United States)

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

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

    Directory of Open Access Journals (Sweden)

    Yukimasa Matsumura

    2012-01-01

    Full Text Available 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 prevent forming pores at the region of laser irradiation and flat surface was fabricated. We also demonstrated that a combination structure with two pore sizes and flat surface was produced by a single laser-pulse irradiation. Our method is a unique microfabrication processing technique that combines the advantages of bottom-up and top-down techniques. This method is a promising technique that can be applied to produce for photonic crystals, biological cell culturing, surface science and electronics fields, and so forth.

  12. Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms

    Science.gov (United States)

    Taylor, Gregory K.; Stoddard, Barry L.

    2012-01-01

    Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of phage, bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that collectively span four distinct nuclease catalytic motifs, have been characterized to date. Members of each family display structural homology and functional relationships to a wide variety of proteins from various organisms. The biological functions of those proteins are highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases, DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These relationships suggest that modern day HEs share common ancestors with proteins involved in genome fidelity, maintenance and gene expression. This review summarizes the results of structural studies of HEs and corresponding proteins from host organisms that have illustrated the manner in which these factors are related. PMID:22406833

  13. Aligning the Band Structures of Polymorphic Molybdenum Oxides and Organic Emitters in Light-Emitting Diodes

    Science.gov (United States)

    Yun, Jongmin; Jang, Woosun; Lee, Taehun; Lee, Yonghyuk; Soon, Aloysius

    2017-02-01

    Heavy transition-metal oxides are widely studied for key applications in electronics and energy technologies. In cutting-edge organic-light-emitting-diode (OLED) devices, there remain scientific challenges to achieve an efficient transfer of charges between electrodes and the organic layer. Recently, polymorphic MoO3 has been actively investigated to exploit its unique high work-function values, especially for its use in the electrode buffer layer to effectively transfer the charges in OLED devices. However, no systematic fundamental studies of its electronic structure are available. Thus, in this study, we use first-principles density-functional theory to investigate both the crystal structure and the electronic structure of the MoO3 polymorphs, and we conclude with a simple perspective to screen the best candidate for OLED applications via a hole transport-barrier descriptor.

  14. Synthesis, Crystal Structure, and Comparative Study of a New Organic Material 3,4-Diaminobenzophenone Semihydrate

    Directory of Open Access Journals (Sweden)

    Tarek Ben Rhaiem

    2013-01-01

    Full Text Available The new organic 3,4-diaminobenzophenone semihydrate (34ABPH is grown by slow evaporation method. The compound crystallizes in the monoclinic space group: C2. The unit cell dimensions are (8 Å, (2 Å, (10 Å, and β = 99.40 (2° with . The crystal structure analysis reveals that the C13H12N2O molecules chains are organized into a double ribbon in the (b,c plane. The structural components interact by N–H⋯O and O–H⋯O hydrogen bonds, building up a two-dimensional network. The presence of functional groups in the molecular structure is confirmed by the Fourier transform infrared (FT-IR spectroscopy. Thermogravimetric analysis (TGA confirms the presence of the water molecule.

  15. Covalent organic frameworks: a materials platform for structural and functional designs

    Science.gov (United States)

    Huang, Ning; Wang, Ping; Jiang, Donglin

    2016-10-01

    Covalent organic frameworks (COFs) are a class of crystalline porous polymer that allows the atomically precise integration of organic units into extended structures with periodic skeletons and ordered nanopores. One important feature of COFs is that they are designable; that is, the geometry and dimensions of the building blocks can be controlled to direct the topological evolution of structural periodicity. The diversity of building blocks and covalent linkage topology schemes make COFs an emerging materials platform for structural control and functional design. Indeed, COF architectures offer confined molecular spaces for the interplay of photons, excitons, electrons, holes, ions and guest molecules, thereby exhibiting unique properties and functions. In this Review, we summarize the major progress in the field of COFs and recent achievements in developing new design principles and synthetic strategies. We highlight cutting-edge functional designs and identify fundamental issues that need to be addressed in conjunction with future research directions from chemistry, physics and materials perspectives.

  16. 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.

  17. Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing.

    Science.gov (United States)

    Forsyth, Charles M; Juan, Veronica; Akamatsu, Yoshiko; DuBridge, Robert B; Doan, Minhtam; Ivanov, Alexander V; Ma, Zhiyuan; Polakoff, Dixie; Razo, Jennifer; Wilson, Keith; Powers, David B

    2013-01-01

    We developed a method for deep mutational scanning of antibody complementarity-determining regions (CDRs) that can determine in parallel the effect of every possible single amino acid CDR substitution on antigen binding. The method uses libraries of full length IgGs containing more than 1000 CDR point mutations displayed on mammalian cells, sorted by flow cytometry into subpopulations based on antigen affinity and analyzed by massively parallel pyrosequencing. Higher, lower and neutral affinity mutations are identified by their enrichment or depletion in the FACS subpopulations. We applied this method to a humanized version of the anti-epidermal growth factor receptor antibody cetuximab, generated a near comprehensive data set for 1060 point mutations that recapitulates previously determined structural and mutational data for these CDRs and identified 67 point mutations that increase affinity. The large-scale, comprehensive sequence-function data sets generated by this method should have broad utility for engineering properties such as antibody affinity and specificity and may advance theoretical understanding of antibody-antigen recognition.

  18. 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.

  19. "Structuration" by Intellectual Organization: The Configuration of Knowledge in Relations among Structural Components in Networks of Science

    CERN Document Server

    Leydesdorff, Loet

    2010-01-01

    Using aggregated journal-journal citation networks, the measurement of the knowledge base in empirical systems is factor-analyzed in two cases of interdisciplinary developments during the period 1995-2005: (i) the development of nanotechnology in the natural sciences and (ii) the development of communication studies as an interdiscipline between social psychology and political science. The results are compared with a case of stable development: the citation networks of core journals in chemistry. These citation networks are intellectually organized by networks of expectations in the knowledge base at the specialty (that is, above-journal) level. This "structuration" of structural components (over time) can be measured as configurational information. The latter is compared with the Shannon-type information generated in the interactions among structural components: the difference between these two measures provides us with a measure for the redundancy generated by the specification of a model in the knowledge b...

  20. 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

  1. Structural and chemical control in assembly of multicomponent metal-organic coordination networks on a surface.

    Science.gov (United States)

    Shi, Ziliang; Lin, Nian

    2010-08-11

    Surface-supported supramolecular self-assembly has been used to generate multicomponent two-dimensional metal-organic coordination networks on a Au(111) surface. The networks consist of linker ligands of 4',4''''-(1,4-phenylene)bis(2,2':6',2''-terpyridine) and nodal ligands of 5,10,15,20-tetra(4-pyridyl)porphyrin that are connected by pyridine-Fe-terpyridine motifs. Scanning tunneling microscopy revealed the coexistence of two polymorphic types of network structures (rhombus and Kagome). Through control of the dosage of the constituent ligands, homogeneous structural phases were obtained selectively. In particular, the rhombus structure could be converted into the more complex and more open Kagome structure by inclusion of guest molecules. Finally, coordination networks providing structural and chemical homogeneity were realized by judiciously choosing the dosages of the constituent ligands and the chemical substitution of the porphyrin ligands.

  2. Evidence of organic structures in Ediacara-type fossils and associated microbial mats

    Science.gov (United States)

    Steiner, Michael; Reitner, Joachim

    2001-12-01

    Ediacara-type fossils represent a group of soft-bodied organisms, mainly known from imprints in Proterozoic coarse-grained siliciclastic sedimentary rocks. Circular compressions of Beltanelliformis brunsae and remains related to Ediacara-type fossils, such as Cucullus fraudulentus, and Mucuplagum primitivum are reported here in an organic mode of preservation from the Neoproterozoic Doushantuo and Liulaobei Formations of China. They can be interpreted as prokaryotic colonies. A charnid fossil with circular attachment disc and stalk, but torn-off frond, is documented in a three-dimensional and partly organic mode of preservation from the Neoproterozoic Ust-Pinega Formation (White Sea coast, Russia). According to their morphology and structure, the Charniidae are not regarded by us as pennatulaceans. Modern Myxobacteria illustrate that macroscopic size, complexity, and even compartmentalization can also be developed by prokaryotic colonies. Part of the Ediacara-type fossils may therefore represent prokaryotic colonies or symbiotic organisms involving prokaryotes. Finally, direct evidence indicates that biofilms with associated prokaryotic sheaths, preserved in both organic and pyritic fashion, form the wrinkled surfaces (“elephant skin”) that were preferentially colonized by Ediacara-type fossils. This finding supports previous interpretations, based on comparative morphological and sedimentological approaches, that ancient wrinkle structures were microbial mats.

  3. Photophysical and electrochemical properties, and molecular structures of organic dyes for dye-sensitized solar cells.

    Science.gov (United States)

    Ooyama, Yousuke; Harima, Yutaka

    2012-12-21

    Dye-sensitized solar cells (DSSCs) based on organic dyes adsorbed on oxide semiconductor electrodes, such as TiO(2), ZnO, or NiO, which have emerged as a new generation of sustainable photovoltaic devices, have attracted much attention from chemists, physicists, and engineers because of enormous scientific interest in not only their construction and operational principles, but also in their high incident-solar-light-to-electricity conversion efficiency and low cost of production. To develop high-performance DSSCs, it is important to create efficient organic dye sensitizers, which should be optimized for the photophysical and electrochemical properties of the dyes themselves, with molecular structures that provide good light-harvesting features, good electron communication between the dye and semiconductor electrode and between the dye and electrolyte, and to control the molecular orientation and arrangement of the dyes on a semiconductor surface. The aim of this Review is not to make a list of a number of organic dye sensitizers developed so far, but to provide a new direction in the epoch-making molecular design of organic dyes for high photovoltaic performance and long-term stability of DSSCs, based on the accumulated knowledge of their photophysical and electrochemical properties, and molecular structures of the organic dye sensitizers developed so far.

  4. Impact of coal structural heterogeneity on the nonideal sorption of organic contaminants.

    Science.gov (United States)

    Shi, Xin; Fu, Heyun; Li, Yuan; Mao, Jingdong; Zheng, Shourong; Zhu, Dongqiang

    2011-06-01

    Carbonaceous geosorbents (black carbon, coal, and humin/kerogen) play a primary role in the nonideal sorption (isotherm nonlinearity, hysteresis, and multiphasic kinetics) of hydrophobic organic chemicals by soils and sediments. The present study investigated the impact of coal structural heterogeneity on sorption/desorption of two model monoaromatic compounds (1,3-dichlorobenzene and 1,3-dinitrobenzene). Due to the higher degree of aromaticity and condensation, anthracite showed stronger sorption affinity and nonlinearity and slower sorption kinetics than lignite. Removal of humic substances by alkali extraction and/or mineral fraction by acidification did not much affect organic carbon-normalized sorption coefficient to the coal, suggesting nearly complete accessibility of adsorption sites on the condensed organic carbon. However, the treatments greatly increased sorption kinetics and meanwhile alleviated hysteresis of 1,3-dinitrobenzene, as compared with the original lignite. These observations were attributed to the enhanced exposure of high-energy adsorption sites on the condensed organic carbon after exfoliating the surface coverage by humic substances and minerals. An empirical biphasic pseudo-second-order model consisting of a fast sorption phase and a slow sorption phase adequately quantified the overall sorption kinetics for the coal sorbents. The results indicated that the condensed organic carbon, in combination with other structural components, controls the nonideal sorption of unburned coal. Copyright © 2011 SETAC.

  5. Self-assembly of metal-organic coordination structures on surfaces

    Science.gov (United States)

    Dong, Lei; Gao, Zi'Ang; Lin, Nian

    2016-08-01

    Metal-organic coordination structures are materials comprising reticular metal centers and organic linkers in which the two constituents bind with each other via metal-ligand coordination interaction. The underlying chemistry is more than a century old but has attracted tremendous attention in the last two decades owing to the rapidly development of metal-organic (or porous coordination) frameworks. These metal-coordination materials exhibit extraordinarily versatile topologies and many potential applications. Since 2002, this traditionally three-dimensional chemistry has been extended to two-dimensional space, that is, to synthesize metal-organic coordination structures directly on solid surfaces. This endeavor has made possible a wide range of so-called surface-confined metal-organic networks (SMONs) whose topology, composition, property and function can be tailored by applying the principle of rational design. The coordination chemistry manifests unique characteristics at the surfaces, and in turn the surfaces provide additional control for design structures and properties that are inaccessible in three-dimensional space. In this review, our goal is to comprehensively cover the progress made in the last 15 years in this rapidly developing field. The review summarizes (1) the experimental and theoretical techniques used in this field including scanning tunneling microscopy and spectroscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, density functional theory, and Monte Carlo and kinetic Monte Carlo simulation; (2) molecular ligands, metal atoms, substrates, and coordination motifs utilized for synthesizing SMON; (3) representative SMON structures with different topologies ranging from finite-size discrete clusters to one-dimensional chains, two-dimensional periodical frameworks and random networks; and (4) the properties and potential applications of SMONs. We conclude the review with some perspectives.

  6. Catchment structure that supports organic matter providing a natural control on rising river nutrient concentrations

    Science.gov (United States)

    Stutter, Marc; Ibiyemi, Adekunle; Wang, Chen

    2017-04-01

    The connectivity of sources of pollution in catchments has been well studied and brings concepts such as pollution hotspots and critical source areas. However, consideration of the placement of other structures combating rising pollution impacts has been less considered. One such area that is receiving developing focus is the layout of riparian management and buffer strips. However, there are wider aspects of connectivity and landscape structure that can bring benefits to delivery and in-stream processing of pollution. These include wetlands, forests and the distribution of soils of differing connectivity of organic matter varying in bioavailability. Organic matter is a great modulator of catchment processes from controlling the potential of land use (e.g. constraints of soil organic matter and wetness on agricultural use), to the amount and form of nutrients leached from soils, to controls of dissolved organic matter on in-stream biology that responds to nutrient concentrations. As the fundamental control of ecosystem energy available for many heterotrophic processes it mediates uptake, recycling and speciation of N, P at many stages of the catchment from soils to waters; as such DOM can be considered as a nature-based solution exerting a background level of control on inorganic nutrients. This poster explores the role of different structural aspects of catchments that provide beneficial organic matter inputs to rivers. At the fine scale the lability of riparian soil and leaf litter DOC are considered. At a riparian management scale the local changes in buffer strip soil C and DOC relative to field soils are considered. At the largest scale spatial data are explored for riparian structure, forests, wetlands and soils differing in delivery and forms of C across major Scottish rivers and used as co-variates to explain differences in in-stream processing of nutrients.

  7. 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.

  8. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Peter E Chen

    Full Text Available BACKGROUND: The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases that survival may be markedly improved by administration of antimicrobial therapy during the early symptomatic phase of the illness; i.e., within 3 days of appearance of symptoms. Microbiological detection methods are feasible only for organisms that can be cultured in vitro and cannot detect all genetic modifications with the exception of antibiotic resistance. Currently available immuno or nucleic acid-based rapid detection assays utilize known, organism-specific proteins or genomic DNA signatures respectively. Hence, these assays lack the ability to detect novel natural variations or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic resistant or virulence enhanced Bacillus anthracis, to advise on therapeutic treatments. METHODOLOGY/PRINCIPAL FINDINGS: We show here that the Roche 454-based pyrosequencing can generate whole genome draft sequences of deep and broad enough coverage of a bacterial genome in less than 24 hours. Furthermore, using the unfinished draft sequences, we demonstrate that unbiased identification of known as well as heretofore-unreported genetic modifications that include indels and single nucleotide polymorphisms conferring antibiotic and phage resistances is feasible within the next 12 hours. CONCLUSIONS/SIGNIFICANCE: Second generation sequencing technologies have paved the way for sequence-based rapid identification of both known and previously undocumented genetic modifications in cultured, conventional and newly emerging biothreat agents. Our findings have significant implications in

  9. Imprinting the surface of mesoporous aluminosilicates using organic structure-directing agents

    Science.gov (United States)

    Sawant, Kaveri R.

    Combining the positive structural features of mesoporous materials and microporous zeolite aluminosilicates can lead to the synthesis and application of new materials useful for catalytic processes involving large organic reactant molecules. We used organic structure-directing agents (SDAs), typically used for the synthesis of zeolites, to imprint the surface of existing mesoporous materials to create novel materials with enhanced structural properties towards this aim: materials with large well-ordered pores allowing access to large reactants with strong accessible acid sites on the surface of the pores leading to stable and active catalysts. We developed new protocols for incorporating tetrapropyl ammonium and N,N,N-trimethyl-1-adamantylammonium, SDAs used for the synthesis of the zeolites ZSM-5 (MFI) and MCM-22 (MWW) respectively, into the walls of the siliceous mesoporous material SBA-15 by using a combination of an organic solvent (glycerol) and water, to form novel porous materials. We studied the evolution of the modified pore structure of the materials by a battery of characterization techniques. Results indicate that the new materials have well-ordered pores with significantly larger mesopore diameters and structurally modified thinner, denser pore walls. We carried out similar treatments and characterization on the aluminum containing form of SBA-15, Al-SBA-15, with high and low amounts of aluminum. Pair distribution function analysis was used to analyze the structural differences in the materials and catalytic test reactions such as cumene and n-hexane cracking to detect the presence of strong acid sites like the ones in ZSM-5. Results similar to the treatments on the all-silica materials, although promising, led to novel meso-micro aluminosilicate materials with limited increase in or no catalytic activity with reference to the test reactions employed. This led to the conclusion that the aluminum in the materials was merely a spectator and did not

  10. Asymmetric PCR method in generation of HBV ssDNA for pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Objective To explore the optimal primer ratio and concentration of asymmetric polymerase chain reaction (A-PCR) in producing hepatitis B virus (HBV) single-stranded DNA (ssDNA) for pyrosequencing. Methods A-PCR was carried out to generate HBV ssDNA with forward to reverse primers of different ratios (50∶1, 100∶1) and concentrations (13.0 pmol/25μL and 0.14 pmol/25μL, 19.5 pmol/25μL and 0.21 pmol/25μL), and the product yield and quality were compared respectively. Results The forward to reverse primer ratio ...

  11. Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing.

    Science.gov (United States)

    Armougom, F; Bittar, F; Stremler, N; Rolain, J-M; Robert, C; Dubus, J-C; Sarles, J; Raoult, D; La Scola, B

    2009-09-01

    Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.

  12. Structural organization and dynamics of exopolysaccharide matrix and microcolonies formation by Streptococcus mutans in biofilms.

    Science.gov (United States)

    Xiao, J; Koo, H

    2010-06-01

    To investigate the structural organization and dynamics of exopolysaccharides (EPS) matrix and microcolonies formation by Streptococcus mutans during the biofilm development process. Biofilms of Strep. mutans were formed on saliva-coated hydroxyapatite (sHA) discs in the presence of glucose or sucrose (alone or mixed with starch). At specific time points, biofilms were subjected to confocal fluorescence imaging and computational analysis. EPS matrix was steadily formed on sHA surface in the presence of sucrose during the first 8 h followed by a threefold biomass increase between 8 and 30 h of biofilm development. The initial formation and further development of three-dimensional microcolony structure occurred concomitantly with EPS matrix synthesis. Tridimensional renderings showed EPS closely associated with microcolonies throughout the biofilm development process forming four distinct domains (i) between sHA surface and microcolonies, (ii) within, (iii) covering and (iv) filling the spaces between microcolonies. The combination of starch and sucrose resulted in rapid formation of elevated amounts of EPS matrix and faster assembly of microcolonies by Strep. mutans, which altered their structural organization and susceptibility of the biofilm to acid killing (vs sucrose-grown biofilms; P matrix and microcolonies provide a more precise examination of the structural organization of biofilms than labelling bacteria alone, which could be a useful approach to elucidate the exact mechanisms by which Strep. mutans influences oral biofilm formation and possibly identify novel targets for effective antibiofilm therapies.

  13. 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.

  14. 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

  15. Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy

    Science.gov (United States)

    Nishida, Jun; Tamimi, Amr; Fei, Honghan; Pullen, Sonja; Ott, Sascha; Cohen, Seth M.; Fayer, Michael D.

    2014-01-01

    The structural elasticity of metal–organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer. PMID:25512539

  16. Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

    Science.gov (United States)

    Prasanna, M. D.; Row, T. N. Guru

    2001-05-01

    The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

  17. 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

    2017-08-11

    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.

  18. Proton Conduction in Sulfonated Organic-Inorganic Hybrid Monoliths with Hierarchical Pore Structure.

    Science.gov (United States)

    von der Lehr, Martin; Seidler, Christopher F; Taffa, Dereje H; Wark, Michael; Smarsly, Bernd M; Marschall, Roland

    2016-09-28

    Porous organic-inorganic hybrid monoliths with hierarchical porosity exhibiting macro- and mesopores are prepared via sol-gel process under variation of the mesopore size. Organic moieties in the pore walls are incorporated by substituting up to 10% of the silicon precursor tetramethylorthosilicate with bisilylated benzene molecules. After functionalization with sulfonic acid groups, the resulting sulfonated hybrid monoliths featuring a bimodal pore structure are investigated regarding proton conduction depending on temperature and relative humidity. The hierarchical pore system and controlled mesopore design turn out to be crucial for sulfonation and proton conduction. These sulfonated hybrid hierarchical monoliths containing only 10% organic precursor exhibit higher proton conduction at different relative humidities than sulfonated periodic mesoporous organosilica made of 100% bisilylated precursors exhibiting solely mesopores, even with a lower concentration of sulfonic acid groups.

  19. 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.

  20. Theoretical description of structural and electronic properties of organic photovoltaic materials.

    Science.gov (United States)

    Zhugayevych, Andriy; Tretiak, Sergei

    2015-04-01

    We review recent progress in the modeling of organic solar cells and photovoltaic materials, as well as discuss the underlying theoretical methods with an emphasis on dynamical electronic processes occurring in organic semiconductors. The key feature of the latter is a strong electron-phonon interaction, making the evolution of electronic and structural degrees of freedom inseparable. We discuss commonly used approaches for first-principles modeling of this evolution, focusing on a multiscale framework based on the Holstein-Peierls Hamiltonian solved via polaron transformation. A challenge for both theoretical and experimental investigations of organic solar cells is the complex multiscale morphology of these devices. Nevertheless, predictive modeling of photovoltaic materials and devices is attainable and is rapidly developing, as reviewed here.

  1. The influence of long term sound stress on histological structure of immune organs in broiler chickens

    Directory of Open Access Journals (Sweden)

    Žikić Dragan R.

    2010-01-01

    Full Text Available The aim of this paper was to examine the effect of different duration sound stress on immune organs of broiler chickens of different age. Nine groups, with 10 chickens in each group were included in experiment. The histological structure of bursa of Fabricius, thymus, and spleen were analyzed. The results indicated that the bursa of Fabricius, in relation to the other examined organs, was the most sensitive to this kind of stress. Histological changes of spleen and thymus were also observed, but less prominent except in chickens after more than 30 days of exposure to stress. According to our results, degree of histological changes of immune organs under the influence of sound stress depends on the length of exposure and age of chickens.

  2. Course of organized structures in thermal plasma inside and outside argon plasma torch

    Science.gov (United States)

    Gruber, Jan; Sonsky, Jiri; Hlina, Jan

    2016-09-01

    Arc chamber of direct-current (dc) argon plasma torch and area just above the nozzle outside of this dc plasma torch were observed by hi-speed camera. System of reflecting mirrors and transparent silica arc chamber walls were used to obtain simultaneous records of both i) cathode area with electric arc inside the plasma torch and ii) nozzle exit with resulting plasma jet outside the plasma torch. Such experimental arrangement allowed us to track localized repeating patterns (organized structures) in the arc chamber and in the plasma flow. Identification of various organized structures - for different experimental conditions - according to their origin and typical development is presented in this paper. Impact of 300 Hz ripple in arc current was compared between different areas of the plasma. Additional simultaneous observation of plasma flow in the same system by series of photodiodes was used for verification of the results. The work was possible with institutional support RVO:61388998.

  3. 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.

  4. Surface reconstruction of abdominal organs using laparoscopic structured light for augmented reality

    Science.gov (United States)

    Ackerman, Jeremy D.; Keller, Kurtis; Fuchs, Henry

    2002-03-01

    Creation of accurate surface models of abdominal organs is essential for many developing technologies in medicine and surgery. One application we are working towards is augmented reality (AR) visualization for laparoscopic surgery. Our current system meets some, but not all, of the requirements. We use two custom built laparoscopes, a custom built miniature projector, a standard camera, and a standard video capture and processing card to implement a laparoscopic structured light range acquisition system. We will briefly show the custom hardware but will emphasize the structured light depth extraction techniques used for the unique properties of surfaces inside the body, particularly dealing with specular reflections. In early experiments, we studied the effectiveness of our algorithm in highly specular environments by creating range images acquired from fresh animal organs. These experiments used a large projector, open abdomens, and offline image processing. We report the results of experiments using our miniature projector, and on line processing.

  5. Imaging the noncentrosymmetric structural organization of tendon with Interferometric Second Harmonic Generation microscopy.

    Science.gov (United States)

    Rivard, Maxime; Popov, Konstantin; Couture, Charles-André; Laliberté, Mathieu; Bertrand-Grenier, Antony; Martin, François; Pépin, Henri; Pfeffer, Christian P; Brown, Cameron; Ramunno, Lora; Légaré, François

    2014-08-01

    We report the imaging of tendon with Interferometric Second Harmonic Generation microscopy. We observe that the noncentrosymmetric structural organization can be maintained along the fibrillar axis over more than 150 μm, while in the transverse direction it is ∼1-15 μm. Those results are explained by modeling tendon as a heterogeneous distribution of noncentrosymmetric nano-cylinders (collagen fibrils) oriented along the fibrillar axis. The preservation of the noncentrosymmetric structural organization over multiple tens of microns reveals that tendon is made of domains in which the ratio between fibrils with positive and negative polarity is unbalanced. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Selective extraction of PAHs from a sediment with structural preservation of Natural Organic Matter.

    Science.gov (United States)

    Merdy, Patricia; Achard, Romain; Samaali, Ismahen; Lucas, Yves

    2014-07-01

    Selective extraction of Polycyclic Aromatic Hydrocarbons (PAH) without structural modification of the Natural Organic Matter (NOM) from a heavily contaminated sediment was investigated using various solvents mixtures. Structural modification of the NOM was monitored after extraction using 3D-fluorescence spectroscopy. Better results were obtained with a 15-h PAH extraction under reflux with a dichloromethane/cyclohexane 20/80 mixture. The experimental procedure was validated with NOM standard materials before to be applied on natural sediments. It could be applied to any environmental solid sample such as sediments and soils. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Carbon frameworks as scaffolding for self-assembly to bio-organic structures

    Science.gov (United States)

    Heinz, Bettina

    1999-12-01

    Carbon spheres and tubes form readily under a variety of physical-chemical conditions. They can mimic elementary life forms as well as fossilized organisms. However, they may still be connected to living systems either as proto- structures for future life or as rudimentary forms of past life. This paper suggests that carbon frameworks allow by virtue of their scaffolding properties the self-assembly to expanded structures, eventually leading to biosystems such as simple viruses and other microorganisms. This development is not limited to terrestrial environments, although solvents molecules such as water and coordinating metal ions are essential vehicles for morphogenesis.

  8. Ion beam assisted deposition of organic molecules: a physical way to realize OLED structures

    Science.gov (United States)

    Moliton, André; Antony, Rémi; Troadec, David; Ratier, Bernard

    2000-05-01

    We demonstrate how the quantum efficiency of an organic light-emitting diode can be improved by a physical way based on the ion beam assisted deposition: the recombination current can be increased by an enhancement of the minority carrier injection while the total current can be decreased by generation of electron traps which reduced the majority current. The quantum efficiency of fluorescence can be also improved by a layer densification with a limitation of the nonradiative centers. As a result, the quantum efficiency of the structure ITO/Helium assisted Alq3/unassisted Alq3/Ca/Al is improved (by around a factor 10) in relation with a virgin structure.

  9. Gold Nanoparticle Self-Similar Chain Structure Organized by DNA Origami

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Baoquan; Deng, Zhengtao; Yan, Hao; Cabrini, Stefano; Zuckermann, Ronald N.; Bokor, Jeffrey

    2010-03-17

    Here we demonstrate Au nanoparticle self-similar chain structure organized by triangle DNA origami with well-controlled orientation and <10 nm spacing. We show for the first time that a large DNA complex (origami) and multiple AuNP conjugates can be well-assembled and purified with reliable yields. The assembled structure could be used to generate high local-field enhancement. The same method can be used to precisely localize multiple components on a DNA template for potential applications in nanophotonic, nanomagnetic, and nanoelectronic devices.

  10. Syllabic organization and deafness: orthographic structure or letter frequency in reading?

    Science.gov (United States)

    Olson, A C; Nickerson, J F

    2001-05-01

    For hearing people, structure given to orthographic information may be influenced by phonological structures that develop with experience of spoken language. In this study we examine whether profoundly deaf individuals structure orthographic representation differently. We ask "Would deaf students who are advanced readers show effects of syllable structure despite their altered experience of spoken language, or would they, because of reduced influence from speech, organize their orthographic knowledge according to groupings defined by letter frequency?" We used a task introduced by Prinzmetal (Prinzmetal, Treiman, & Rho, 1986) in which participants were asked to judge the colour of letters in briefly presented words. As with hearing participants, the number of errors made by deaf participants was influenced by syllable structure (Prinzmetal et al., 1986; Rapp, 1992). This effect could not be accounted for by letter frequency. Furthermore, there was no correlation between the strength of syllable effects and residual speech or hearing. Our results support the view that the syllable is a unit of linguistic organization that is abstract enough to apply to both spoken and written language.

  11. Doing the Organizational Tango: Symbiotic Relationship between Formal and Informal Organizational Structures for an Agile Organization

    Directory of Open Access Journals (Sweden)

    Irena Malgorzata Ali

    2016-04-01

    Full Text Available This paper reports on research with a broad objective to examine the relationship between two organizational entities, the formally structured organization and informal organizational structures, in a changing operational environment, more specifically during military deployments. The paper draws on organizational and complexity paradigms; based on empirical evidence obtained through qualitative techniques, it describes mechanisms that enable a symbiotic relationship between these two organizational structures in a complex operational landscape. Substantive findings provide insights into the dynamics of the interactions between these structures and illuminate the relationship between three enabling factors – accountability, responsible autonomy, and command and control arrangements – that need to be considered to fully exploit the strengths inherent in both formal and informal structures. Based on these findings, a model for enhancement of organizational agility in response to changes in a complex operational environment is described. The model is predicated on feedback and mutual adjustment of the organization, institution and individual through sensemaking; it illustrates the dynamic nature of interactions that are required for such a response.

  12. Controlled synthesis of organic nanophotonic materials with specific structures and compositions.

    Science.gov (United States)

    Cui, Qiu Hong; Zhao, Yong Sheng; Yao, Jiannian

    2014-10-29

    Organic nanomaterials have drawn great interest for their potential applications in high-speed miniaturized photonic integration due to their high photoluminescence quantum efficiency, structural processability, ultrafast photoresponse, and excellent property engineering. Based on the rational design on morphological and componential levels, a series of organic nanomaterials have been controllably synthesized in recent years, and their excitonic/photonic behaviors has been fine-tuned to steer the light flow for specific optical applications. This review presents a comprehensive summary of recent breakthroughs in the controlled synthesis of organic nanomaterials with specific structures and compositions, whose tunable photonic properties would provide a novel platform for multifunctional applications. First, we give a general overview of the tailored construction of novel nanostructures with various photonic properties. Then, we summarize the design and controllable synthesis of composite materials for the modulation of their functionalities. Subsequently, special emphasis is put on the fabrication of complex nanostructures towards wide applications in isolated photonic devices. We conclude with our personal viewpoints on the development directions in the novel design and controllable construction of organic nanomaterials for future applications in highly integrated photonic devices and chips.

  13. Pyrosequencing analysis for mutations in embB codon306 among clinical mycobacterium tuberculosis isolates from Qingdao, China.

    Science.gov (United States)

    Zhang, Huaqiang; Chen, Xiaoguang; Wang, Zhongdong; Ren, Zhisheng; Wu, Jie; Sun, Haiyan; Bai, Xue

    2015-01-01

    In this study, our objectives was to analyze the molecular characteristics of mutation at embB codon306 in Mycobacterium tuberculosis in Qingdao by pyrosequencing technology, and to assess the value of embB codon306 used as a molecular marker to diagnose multidrug resistant (MDR) TB strains. Pyrosequencing was used to detect mutations at embB codon306 among M. tuberculosis isolates from tuberculosis (TB) patients in Qingdao. The correlation between embB306 mutation and MDR phenotype was evaluated by comparing with conventional drug susceptibility testing results. 60.9% of MDR strains and 15.2% of non-MDR strains carried embB306 mutation, respectively. The percentage of MDR-TB harboring embB306 mutation was significantly higher than that of non- MDR-TB (χ(2)=15.09, P Pyrosequencing should be a good diagnostic tool for MDR-TB in Qingdao.

  14. Identification of Atmospheric Organic Matter in Fog Water: Exact Masses, Empirical Formulas, and Structural Insights

    Science.gov (United States)

    Mazzoleni, L. R.; Collett, J. L.

    2009-12-01

    Aqueous processing of organic matter by clouds and fogs may significantly alter aerosol-climate properties. Heterogeneous chemical reactions that serve to promote oxidation of apolar primary emission components may result in an increase of hydrophilic organic compounds, while reactions that serve to promote oligomerization and/or formation of larger components, such as HULIS, may result in a decrease. Since aerosol organic matter is very complex and its identity is not well understood, we chose to study the detailed molecular composition of atmospheric organic matter (AOM) of polluted fogs by ultra-high resolution FT-Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). In all of our analyses, we found a high degree of complexity across the mass range of 100 to 400 u and in some of our analyses we observed our mass range to extend up to 1000 u. The detected negative organic ions were multifunctional compounds which include C, H, N, O, and S elements. We observed organic nitrogen (CHNO), organic sulfur (CHOS), and organic nitrooxy-sulfate compounds (CHNOS) as well as many masses with only CHO elemental composition. Analysis of the atomic valances by double bond equivalents (DBE) calculations suggests that these compound structures range from highly aliphatic to aromatic with DBE values of 1-11, suggesting a wide variety of precursor compounds with variable oxidation states. This resulted in a high degree of complexity in the low mass range which was greatly reduced by data filtering strategies that group assigned formulas into homologous series and oligomeric series with increasing chain lengths. The AOM oligomeric series with formula differences of C3H4O2 are very likely due to an aqueous esterification reaction, originally suggested by Altieri et al., 2008. We found over 400 oligomer series in our dataset, representing approximately 80% of the CHO and CHNO compounds combined. A very high number of homologous series of compounds and polyfunctional oligomers were

  15. Nanoscale Structure of Self-Assembling Hybrid Materials of Inorganic and Electronically Active Organic Phases

    Energy Technology Data Exchange (ETDEWEB)

    Sofos, M.; Goswami, D.A. Stone D.K.; Okasinski, J.S.; Jin, H.; Bedzyk, M.J.; Stupp, S.I. (NWU)

    2008-10-06

    Hybrid materials with nanoscale structure that incorporates inorganic and organic phases with electronic properties offer potential in an extensive functional space that includes photovoltaics, light emission, and sensing. This work describes the nanoscale structure of model hybrid materials with phases of silica and electronically active bola-amphiphile assemblies containing either oligo(p-phenylene vinylene) or oligo(thiophene) segments. The hybrid materials studied here were synthesized by evaporation-induced self-assembly and characterized by X-ray scattering techniques. Grazing-incidence X-ray scattering studies of these materials revealed the formation of two-dimensional hexagonally packed cylindrical micelles of the organic molecules with diameters between 3.1 and 3.6 nm and cylindrical axes parallel to the surface. During the self-assembly process at low pH, the cylindrical aggregates of conjugated molecules become surrounded by silica giving rise to a hybrid structure with long-range order. Specular X-ray reflectivity confirmed the long-range periodicity of the hybrid films within a specific range of molar ratios of tetraethyl orthosilicate to cationic amphiphile. We did not observe any long-range ordering in fully organic analogues unless quaternary ammonium groups were replaced by tertiary amines. These observations suggest that charge screening in these biscationic conjugated molecules by the mineral phase is a key factor in the evolution of long range order in the self-assembling hybrids.

  16. Unraveling the multiscale structural organization and connectivity of the human brain: the role of diffusion MRI

    Directory of Open Access Journals (Sweden)

    Matteo eBastiani

    2015-06-01

    Full Text Available The structural architecture and the anatomical connectivity of the human brain show different organizational principles at distinct spatial scales. Histological staining and light microscopy techniques have been widely used in classical neuroanatomical studies to unravel brain organization. Using such techniques is a laborious task performed on 2-dimensional histological sections by skilled anatomists possibly aided by semi-automated algorithms. With the recent advent of modern magnetic resonance imaging (MRI contrast mechanisms, cortical layers and columns can now be reliably identified and their structural properties quantified post mortem. These developments are allowing the investigation of neuroanatomical features of the brain at a spatial resolution that could be interfaced with that of histology. Diffusion MRI and tractography techniques, in particular, have been used to probe the architecture of both white and gray matter in three dimensions. Combined with mathematical network analysis, these techniques are increasingly influential in the investigation of the macro-, meso- and microscopic organization of brain connectivity and anatomy, both in vivo and ex vivo. Diffusion MRI-based techniques in combination with histology approaches can therefore support the endeavor of creating multimodal atlases that take into account the different spatial scales or levels on which the brain is organized. The aim of this review is to illustrate and discuss the structural architecture and the anatomical connectivity of the human brain at different spatial scales and how recently developed diffusion MRI techniques can help investigate these.

  17. Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool

    Directory of Open Access Journals (Sweden)

    Klopp Christophe

    2011-05-01

    Full Text Available Abstract Background Roche 454 pyrosequencing platform is often considered the most versatile of the Next Generation Sequencing technology platforms, permitting the sequencing of large genomes, the analysis of variations or the study of transcriptomes. A recent reported bias leads to the production of multiple reads for a unique DNA fragment in a random manner within a run. This bias has a direct impact on the quality of the measurement of the representation of the fragments using the reads. Other cleaning steps are usually performed on the reads before assembly or alignment. Findings PyroCleaner is a software module intended to clean 454 pyrosequencing reads in order to ease the assembly process. This program is a free software and is distributed under the terms of the GNU General Public License as published by the Free Software Foundation. It implements several filters using criteria such as read duplication, length, complexity, base-pair quality and number of undetermined bases. It also permits to clean flowgram files (.sff of paired-end sequences generating on one hand validated paired-ends file and the other hand single read file. Conclusions Read cleaning has always been an important step in sequence analysis. The pyrocleaner python module is a Swiss knife dedicated to 454 reads cleaning. It includes commonly used filters as well as specialised ones such as duplicated read removal and paired-end read verification.

  18. Human papillomavirus genotyping by multiplex pyrosequencing in cervical cancer patients from India

    Indian Academy of Sciences (India)

    Cheryl M Travasso; Mona Anand Mansi; Mansi Samarth; Aditi Deshpande; Chandan Kumar-Sinha

    2008-03-01

    Cervical cancer is a leading cause of cancer-related deaths among women in India. Human papillomavirus (HPV) infection is the causative agent of cervical cancer; and infection with the high-risk genotypes, predominantly HPV16 and 18, is the biggest risk factor. Vaccines targeting HPV16 and 18 have been found to confer protection in large-scale clinical trials. HPV genotyping has traditionally been carried out to screen the population “at risk” using indirect methods based on polymerase chain reaction (PCR) using consensus primers combined with various DNA hybridization techniques, and often followed by the sequencing of candidate products. Recently, a high-throughput and direct method based on DNA sequencing has been described for HPV genotyping using multiplex pyrosequencing. We present a pilot study on HPV genotyping of cervical cancer and non-malignant cervical samples using multiplex pyrosequencing. Using genomic DNA from cell lines, cervical biopsies, surgical tissues or formalin-fixed, paraffin-embedded tissue samples, we could successfully resolve 6 different HPV types out of the 7 tested, with their prevalence found to be in agreement with earlier reports. We also resolved coinfections with two different HPV types in several samples. An HPV16 genotype with a specific and recurrent sequence variation was observed in 8 cancer samples and one non-malignant sample. We find this technique eminently suited for high-throughput applications, which can be easily extended to large sample cohorts to determine a robust benchmark for HPV genotypes prevalent in India.

  19. Molecular differentiation of Trichinella spiralis, T. pseudospiralis, T. papuae and T. zimbabwensis by pyrosequencing.

    Science.gov (United States)

    Sadaow, L; Tantrawatpan, C; Intapan, P M; Lulitanond, V; Boonmars, T; Morakote, N; Pozio, E; Maleewong, W

    2015-01-01

    Nematodes of the genus Trichinella which infect wildlife and domestic animals show a cosmopolitan distribution. These zoonotic parasites are the aetiological agents of a severe human disease, trichinellosis. Twelve taxa are recognized in the Trichinella genus, but they cannot be identified by morphology since they are sibling species/genotypes. For epidemiological studies, it is extremely important to identify each taxon since they have different distribution areas and host ranges. In the present study, polymerase chain reaction (PCR) amplification of the mitochondrial large subunit ribosomal RNA (lsu-RNA) gene coupled with a pyrosequencing technique was developed to distinguish among four Trichinella species: Trichinella spiralis, T. pseudospiralis, T. papuae and T. zimbabwensis. A PCR method was used to amplify the lsu-RNA of Trichinella sp. larvae in mouse muscles and single larvae collected from infected muscles by digestion. The results show that the four Trichinella species can be distinguished by using 26 nucleotides in the target region and the method is sensitive enough to identify individual larvae. The pyrosequencing provides a simple, rapid and high-throughput tool for the differentiation of Trichinella species.

  20. Rapid Detection and Identification of Yersinia pestis from Food Using Immunomagnetic Separation and Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Kingsley K. Amoako

    2012-01-01

    Full Text Available Interest has recently been renewed in the possible use of Y. pestis, the causative agent of plague, as a biological weapon by terrorists. The vulnerability of food to intentional contamination coupled with reports of humans having acquired plague through eating infected animals that were not adequately cooked or handling of meat from infected animals makes the possible use of Y. pestis in a foodborne bioterrorism attack a reality. Rapid, efficient food sample preparation and detection systems that will help overcome the problem associated with the complexity of the different matrices and also remove any ambiguity in results will enable rapid informed decisions to be made regarding contamination of food with biothreat agents. We have developed a rapid detection assay that combines the use of immunomagnetic separation and pyrosequencing in generating results for the unambiguous identification of Y. pestis from milk (0.9 CFU/mL, bagged salad (1.6 CFU/g, and processed meat (10 CFU/g. The low detection limits demonstrated in this assay provide a novel tool for the rapid detection and confirmation of Y. pestis in food without the need for enrichment. The combined use of the iCropTheBug system and pyrosequencing for efficient capture and detection of Y. pestis is novel and has potential applications in food biodefence.