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  1. Disease Resistance Gene Analogs (RGAs) in Plants

    PubMed Central

    Sekhwal, Manoj Kumar; Li, Pingchuan; Lam, Irene; Wang, Xiue; Cloutier, Sylvie; You, Frank M.

    2015-01-01

    Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens’ resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed. PMID:26287177

  2. Disease Resistance Gene Analogs (RGAs) in Plants.

    PubMed

    Sekhwal, Manoj Kumar; Li, Pingchuan; Lam, Irene; Wang, Xiue; Cloutier, Sylvie; You, Frank M

    2015-01-01

    Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

  3. Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae family.

    PubMed

    Perazzolli, Michele; Malacarne, Giulia; Baldo, Angela; Righetti, Laura; Bailey, Aubrey; Fontana, Paolo; Velasco, Riccardo; Malnoy, Mickael

    2014-01-01

    The family of resistance gene analogues (RGAs) with a nucleotide-binding site (NBS) domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh.) cultivar 'Golden Delicious'. This represents 1.51% of the total number of predicted genes for this cultivar. Several evolutionary features are pronounced in M. domestica, including a high fraction (80%) of RGAs occurring in clusters. This suggests frequent tandem duplication and ectopic translocation events. Of the identified RGAs, 56% are located preferentially on six chromosomes (Chr 2, 7, 8, 10, 11, and 15), and 25% are located on Chr 2. TIR-NBS and non-TIR-NBS classes of RGAs are primarily exclusive of different chromosomes, and 99% of non-TIR-NBS RGAs are located on Chr 11. A phylogenetic reconstruction was conducted to study the evolution of RGAs in the Rosaceae family. More than 1400 RGAs were identified in six species based on their NBS domain, and a neighbor-joining analysis was used to reconstruct the phylogenetic relationships among the protein sequences. Specific phylogenetic clades were found for RGAs of Malus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, and Prunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.

  4. Characterization of resistance gene analogues (RGAs) in Apple (Malus 6domestica Borkh.) and their evolutionary history of the Rosaceae family

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The family of resistance gene analogues (RGAs) with a nucleotide-binding site (NBS) domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh.) cultivar ‘Golden...

  5. Isolation and characterization of a set of disease resistance-gene analogs (RGAs) from wild rice, Zizania latifolia Griseb. I. Introgression, copy number lability, sequence change, and DNA methylation alteration in several rice-Zizania introgression lines.

    PubMed

    Chen, Yu; Long, Likun; Lin, Xiuyun; Guo, Wanli; Liu, Bao

    2006-02-01

    Eight resistance-gene analogs (RGAs) were isolated from wild rice, Zizania latifolia Griseb., by degenerate primers designed according to conserved motifs at or around the nucleotide-binding site (NBS) of known NBS-containing plant resistance genes. The 8 RGAs were classified into 6 distinct groups based on their deduced amino acid sequence similarity of 60% or greater. Gel-blot hybridization of each of the RGAs to 4 rice - Z. latifolia intro gression lines indicated an array of changes at either introgressed Zizania RGAs or, more likely, their rice homologs. The changes included dramatic increase in copy number, modification at the primary DNA sequence, and alteration in DNA methylation patterns. PMID:16498465

  6. A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs

    PubMed Central

    Sharma, Arun; Zhang, Liping; Niño-Liu, David; Ashrafi, Hamid; Foolad, Majid R.

    2008-01-01

    We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F2 population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum. PMID:19223983

  7. Characterization of expressed resistance gene analogs (RGAs) from peanut expressed sequence tags (ESTs)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated peanut (Arachis hypogaea L.) is one of the most important food legume crops grown worldwide, and is a major source for edible oil and protein. However, due to low genetic variation, peanut is very vulnerable to a variety of pathogens, such as early leaf spot, late leaf spot, rust and Toma...

  8. The CC-NBS-LRR Subfamily in Pinus monticola: Targeted Identification, Gene Expression, and Genetic Linkage with Resistance to Cronartium ribicola.

    PubMed

    Liu, Jun-Jun; Ekramoddoullah, Abul K M

    2007-06-01

    ABSTRACT To investigate disease resistance gene analogs (RGAs) encoding coiled-coil-nucelotide-binding site-leucine-rich repeats (CC-NBS-LRR) proteins in western white pine, degenerate primers targeting the conserved motifs in the NBS domain were designed to amplify RGAs from genomic DNA and cDNA. Sixty-one distinct RGAs were identified with identities to well-known R proteins of the CC-NBS-LRR subfamily. These RGAs exhibited variation of putative amino acid sequences from 13% to 98%, representing a complex CC-NBS-LRR subfamily. A phylogenetic tree constructed from the amino acid sequence alignment revealed that these 61 RGAs were grouped with other CC-NBS-LRR members from angiosperms, and could be further divided into six classes with an identity threshold of 68%. To map RGAs, RGA polymorphisms and a modified amplified fragment length polymorphism (AFLP) method with incorporated sequences from the NBS domain were used to reveal NBS or NBS-AFLP markers. RGA polymorphism study revealed that three off the identified RGAs were not linked to the Cr2 gene imparting resistance to white pine blister rust. However, the AFLP strategy, using bulk segregant analysis (BSA) and haploid segregation analysis, identified 11 NBS-AFLP markers localized in the Cr2 linkage, the closest two to the gene being 0.41 cM and 1.22 cM away at either side. Eight of these markers showed significant amino acid sequence homologies with RGAs. PMID:18943604

  9. Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.).

    PubMed

    Hunger, Sandra; Di Gaspero, Gabriele; Möhring, Slike; Bellin, Diana; Schäfer-Pregl, Ralf; Borchardt, Dietrich C; Durel, Charles-Eric; Werber, Martin; Weisshaar, Bernd; Salamini, Francesco; Schneider, Katharina

    2003-02-01

    Sequence conservation among resistance genes (R genes) was exploited to identify 47 R gene analogues (RGAs) from sugar beet (Beta vulgaris L.). Using degenerate primers, 11 RGAs were amplified from genomic DNA and 7 from leaf or beet cDNA. Twenty-nine were selected from an EST sequencing program. Twenty-one RGAs contained structures similar to the nucleotide binding site (NBS)--leucine rich repeat (LRR) domain, a motif commonly found in several R genes. Among the remaining RGAs, 19 revealed similarity to the serine (threonine) protein kinase domain of R genes, 4 showed features related to the LRR region of the rice disease resistance gene Xa21, 1 RGA resembled the sugar beet nematode resistance gene Hs1pro-1, and 2 had homologies to other gene products associated with disease resistance. For 20 EST-derived RGAs, transcript levels were compared in leaf and root tissue revealing organ-specific transcription in 7 cases. Thirty-three RGAs were spread over all nine sugar beet chromosomes, except for a cluster of nine closely linked RGAs on chromosome 7. The analysis of linkage between RGAs and loci for rhizomania and Cercospora resistance identified alleles associated with resistance in both cases.

  10. Expression, mapping, and genetic variability of Brassica napus disease resistance gene analogues.

    PubMed

    Fourmann, M; Chariot, F; Froger, N; Delourme, R; Brunel, D

    2001-12-01

    Numerous sequences analogous to resistance (R) genes exist in plant genomes and could be involved in resistance traits. The aim of this study was to identify a large number of Brassica napus sequences related to R genes and also to test the adequacy of specific PCR-based tools for studying them. Different consensus primers were compared for their efficiency in amplifying resistance-gene analogues (RGAs) related to the nucleotide-binding-site subgroup of R genes. Specific primers were subsequently designed to fine-study the different RGAs and we tested their efficiency in three species related to B. napus: Brassica oleracea, Brassica rapa, and Arabidopsis thaliana. Forty-four B. napus RGAs were identified. Among 29 examined, at least one-third were expressed. Eighteen RGAs were mapped on 10 of the 19 B. napus linkage groups. The high variability within these sequences permitted discrimination of each genotype within a B. napus collection. The RGA-specific primers amplified RGAs in the B. oleracea and B. rapa genomes, but the sequences appear to be poorly conserved in A. thaliana. Specific RGA primers are a precise tool for studying known-sequence RGAs. These sequences represent interesting markers that could be correlated with resistance traits in B. napus or related Brassica genomes.

  11. Resistance gene analogs involved in tolerant cassava--geminivirus interaction that shows a recovery phenotype.

    PubMed

    Louis, Bengyella; Rey, Chrissie

    2015-12-01

    The current literature describes recovery from virus-induced symptoms as a RNA silencing defense, but immunity-related genes, including the structurally specific resistance gene analogs (RGAs) that may play a key role in tolerance and recovery is not yet reported. In this study, the transcriptome data of tolerant cassava TME3 (which exhibits a recovery phenotype) and susceptible cassava T200 infected with South African cassava mosaic virus were explored for RGAs. Putative resistance protein analogs (RPAs) with amide-like indole-3-acetic acid-Ile-Leu-Arg (IAA-ILR) and leucine-rich repeat (LRR)-kinase conserved domains were unique to TME3. Common responsive RPAs in TME3 and T200 were the dirigent-like protein, coil-coil nucleotide-binding site (NBS) and toll-interleukin-resistance, disease resistance zinc finger chromosome condensation-like protein (DZC), and NBS-apoptosis repressor with caspase recruitment (ARC)-LRR domains. Mutations in RPAs in the MHD motif of the NBS-ARC2 subdomain associated with the recovery phase in TME3 were observed. Additionally, a cohort of 25 RGAs mined solely during the recovery process in TME3 was identified. Phylogenetic and expression analyses support that diverse RGAs are differentially expressed during tolerance and recovery. This study reveals that in cassava, a perennial crop, RGAs participate in tolerance and differentially accumulate during recovery as a complementary defense mechanism to natural occurring RNA silencing to impair viral replication.

  12. Development of RGA-CAPS markers and genetic mapping of candidate genes for sugarcane mosaic virus resistance in maize.

    PubMed

    Quint, M.; Mihaljevic, R.; Dussle, M.; Xu, L.; Melchinger, E.; Lübberstedt, T.

    2002-08-01

    Three previously published resistance gene analogues (RGAs), pic13, pic21 and pic19, were mapped in relation to sugarcane mosaic virus (SCMV) resistance genes ( Scmv1, Scmv2) in maize. We cloned these RGAs from six inbreds including three SCMV-resistant lines (D21, D32, FAP1360A) and three SCMV-susceptible lines (D145, D408, F7). Pairwise sequence alignments among the six inbreds revealed a frequency of one single nucleotide polymorphism (SNP) per 33 bp for the three RGAs, indicating a high degree of polymorphism and a high probability of success in converting RGAs into codominant cleaved amplified polymorphic sequence (CAPS) markers compared to other sequences. SNPs were used to develop CAPS markers for mapping of the three RGAs in relation to Scmv1 (chromosome 6) and Scmv2 (chromosome 3), and for pedigree analyses of resistant inbred lines. By genetic mapping pic21 was shown to be different from Scmv2, whereas pic19 and pic13 are still candidates for Scmv1 and Scmv2, respectively, due to genetic mapping and consistent restriction patterns of ancestral lines.

  13. In situ ultrahigh vacuum residual gas analyzer 'calibration'

    SciTech Connect

    Malyshev, O. B.; Middleman, K. J.

    2008-11-15

    Knowing the residual gas spectrum is essential for many applications and research in ultrahigh vacuum (UHV). Residual gas analyzers (RGAs) are used for both qualitative and quantitative gas analyses, where the quadrupole mass analyzers are now the most popular. It was found that RGAs supplied by different manufacturers are not necessarily well calibrated for quantitative gas analysis. A procedure applied for in situ RGA 'calibration' against a calibrated UHV total pressure gauge is described in this article. It was found that special attention should be paid to H{sub 2} calibration, as RGAs are usually much more sensitive to H{sub 2} than ionization gauges. The calibration coefficients are quite reproducible in Faraday cup mode, however, using the secondary electron multiplier requires frequent checks of the calibration coefficients. The coefficients obtained for the RGA allow the use of the RGA as an accurate device for gas spectrum analysis.

  14. Identification and mapping of resistance gene analogs and a white rust resistance locus in Brassica rapa ssp. oleifera.

    PubMed

    Tanhuanpää, P

    2004-04-01

    The objective of this investigation was to tag a locus for white rust resistance in a Brassica rapa ssp. oleifera F(2) population segregating for this trait, using bulked segregant analysis with random amplified polymorphic DNA (RAPD) markers, linkage mapping and a candidate gene approach based on resistance gene analogs (RGAs). The resistance source was the Finnish line Bor4109. The reaction against white rust races 7a and 7v was scored in 20 seedlings from each self-pollinated F(2 )individual. The proportion of resistant plants among these F(3) families varied from 0 to 67%. Bulked segregant analysis did not reveal any markers linked with resistance and, therefore, a linkage map with 81 markers was created. A locus that accounted for 18.4% of the variation in resistance to white rust was mapped to linkage group (LG) 2 near the RAPD marker Z19a. During the study, a bacterial resistance gene homologous to Arabidopsis RPS2 and six different RGAs were sequenced. RPS2 and five of the RGAs were mapped to linkage groups LG1, LG4 and LG9. Unfortunately, none of the RGAs could be shown to be associated with white rust resistance.

  15. Validation and application of reporter gene assays for the determination of estrogenic and androgenic endocrine disruptor activity in sport supplements.

    PubMed

    Plotan, Monika; Elliott, Christopher T; Oplatowska, Michalina; Connolly, Lisa

    2012-07-01

    Previously developed estrogen and androgen mammalian reporter gene assays (RGAs) were assessed for their potential use as a quantitative screening method in the detection of estrogenic and androgenic endocrine disruptors (EDs) in sport supplements. The validation of both RGAs coupled with dispersive solid phase extraction (dSPE) was performed in accordance with European Commission Decision EC/2002/6579 for biological screening methods. Decision limits (CCα) and detection capabilities (CCβ) were established for both the estrogen and androgen RGAs. All samples were compliant with CCα and CCβ in both bioassays. Recovery rates were 96 % for 17β-estradiol and 115 % for dihydrotestosterone as obtained in their corresponding RGA. Both estrogens and androgens were stable in samples for more than 3 weeks, when stored at -20 °C. Specificity, good repeatability (coefficients of variation (CV), 12-25 %), reproducibility and robustness of both bioassays were also observed. Four different ED modes of action were determined for estrogens and androgens in 53 sport supplements, using the validated RGAs. This study revealed that 89 % of the investigated sport supplements contained estrogenic EDs and 51 % contained androgenic compounds. In conclusion, both bioassays are suitable for sport supplement screening of estrogenic and androgenic EDs.

  16. Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance.

    PubMed

    Palomino, Carmen; Fernández-Romero, M D; Rubio, J; Torres, A; Moreno, M T; Millán, T

    2009-02-01

    A composite linkage map was constructed based on two interspecific recombinant inbred line populations derived from crosses between Cicer arietinum (ILC72 and ICCL81001) and Cicer reticulatum (Cr5-10 or Cr5-9). These mapping populations segregate for resistance to ascochyta blight (caused by Ascochyta rabiei), fusarium wilt (caused by Fusarium oxysporum f. sp. ciceris) and rust (caused by Uromyces ciceris-arietini). The presence of single nucleotide polymorphisms in ten resistance gene analogs (RGAs) previously isolated and characterized was exploited. Six out of the ten RGAs were novel sequences. In addition, classes RGA05, RGA06, RGA07, RGA08, RGA09 and RGA10 were considerate putatively functional since they matched with several legume expressed sequences tags (ESTs) obtained under infection conditions. Seven RGA PCR-based markers (5 CAPS and 2 dCAPS) were developed and successfully genotyped in the two progenies. Six of them have been mapped in different linkage groups where major quantitative trait loci conferring resistance to ascochyta blight and fusarium wilt have been reported. Genomic locations of RGAs were compared with those of known Cicer R-genes and previously mapped RGAs. Association was detected between RGA05 and genes controlling resistance to fusarium wilt caused by races 0 and 5.

  17. Identification of expressed resistance gene analogs from peanut (Arachis hypogaea L.) expressed sequence tags.

    PubMed

    Liu, Zhanji; Feng, Suping; Pandey, Manish K; Chen, Xiaoping; Culbreath, Albert K; Varshney, Rajeev K; Guo, Baozhu

    2013-05-01

    Low genetic diversity makes peanut (Arachis hypogaea L.) very vulnerable to plant pathogens, causing severe yield loss and reduced seed quality. Several hundred partial genomic DNA sequences as nucleotide-binding-site leucine-rich repeat (NBS-LRR) resistance genes (R) have been identified, but a small portion with expressed transcripts has been found. We aimed to identify resistance gene analogs (RGAs) from peanut expressed sequence tags (ESTs) and to develop polymorphic markers. The protein sequences of 54 known R genes were used to identify homologs from peanut ESTs from public databases. A total of 1,053 ESTs corresponding to six different classes of known R genes were recovered, and assembled 156 contigs and 229 singletons as peanut-expressed RGAs. There were 69 that encoded for NBS-LRR proteins, 191 that encoded for protein kinases, 82 that encoded for LRR-PK/transmembrane proteins, 28 that encoded for Toxin reductases, 11 that encoded for LRR-domain containing proteins and four that encoded for TM-domain containing proteins. Twenty-eight simple sequence repeats (SSRs) were identified from 25 peanut expressed RGAs. One SSR polymorphic marker (RGA121) was identified. Two polymerase chain reaction-based markers (Ahsw-1 and Ahsw-2) developed from RGA013 were homologous to the Tomato Spotted Wilt Virus (TSWV) resistance gene. All three markers were mapped on the same linkage group AhIV. These expressed RGAs are the source for RGA-tagged marker development and identification of peanut resistance genes.

  18. Characterization of suspended-sediment transport conditions for stable, “Reference” streams in selected Ecoregions of EPA Region 8

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Historic flow and sediment transport data from about 350 sites across the Mountains and Plains region of the United States were analyzed for the purpose of developing ‘background’ or ‘reference’ rates of suspended-sediment transport by Level III ecoregion. Rapid Geomorphic Assessments (RGAs) were c...

  19. Suspended-Sediment Transport Rates for Level III Ecoregions of EPA Region 4: the Southeast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Historic flow and sediment transport data from about 750 sites across the southeastern United States were analyzed for the purpose of developing "background" or "reference" rates of suspended-sediment transport by Level III ecoregion. Rapid Geomorphic Assessments (RGAs) were conducted at most sites...

  20. Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

    PubMed Central

    2012-01-01

    Background Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family is the largest class of known disease resistance genes (R genes) effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. Results A total of 78 R gene analogues (CaRGAs) were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL) along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR)-NBS-LRR (CaRGAs I to IV) and TIR-NBS-LRR (CaRGAs V to VII) subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain) is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in defence responses by

  1. Thin-walled SnO2 nanotubes functionalized with Pt and Au catalysts via the protein templating route and their selective detection of acetone and hydrogen sulfide molecules

    NASA Astrophysics Data System (ADS)

    Jang, Ji-Soo; Kim, Sang-Joon; Choi, Seon-Jin; Kim, Nam-Hoon; Hakim, Meggie; Rothschild, Avner; Kim, Il-Doo

    2015-10-01

    Bio-inspired Pt (~2 nm) and Au (~2.7 nm) catalysts encapsulated by a protein shell, i.e., Pt-apoferritin (Pt@AF) and Au-apoferriten (Au@AF), were synthesized via the hollow protein nanocage (apoferritin) templating route and directly functionalized on the interior and exterior walls of electrospun SnO2 nanotubes (NTs) during controlled single-nozzle electrospinning followed by high temperature calcination with heating rate control. Fast crystallization of the exterior shell and outward diffusion of the interior Sn precursors and crystallites result in the continued growth of a tubular wall, which is related to rapid heating driven Ostwald-ripening behavior. Very importantly, the Pt and Au nanoparticles (NPs) were immobilized onto thin-walled SnO2 NTs with a diameter of ~350 nm and a shell thickness of ~40 nm without any aggregation of catalysts due to high dispersibility, which originated from repulsive electrostatic (Coulombic) forces acting on the surface charged protein shells, leading to an enhanced catalytic effect and outstanding gas sensing properties. Pt-loaded SnO2 NTs exhibited superior acetone response (Rair/Rgas = 92 at 5 ppm) compared to pure SnO2 NFs (Rair/Rgas = 4.8 at 5 ppm) and SnO2 NTs (Rair/Rgas = 11 at 5 ppm) while Au-loaded SnO2 NTs showed a high response when exposed to hydrogen sulfide (Rair/Rgas = 34 at 5 ppm), offering selective gas detection with minimal cross-sensitivity against other interfering gases such as NH3, CO, NO, C6H5CH3, and C5H12. Our results provide a new insight into facile, cost-effective, and highly dispersible catalyst loading on the interior and exterior walls of hollow metal oxide NTs via simple electrospinning as a potential breath analyzer.Bio-inspired Pt (~2 nm) and Au (~2.7 nm) catalysts encapsulated by a protein shell, i.e., Pt-apoferritin (Pt@AF) and Au-apoferriten (Au@AF), were synthesized via the hollow protein nanocage (apoferritin) templating route and directly functionalized on the interior and exterior walls

  2. Evaluation of low cost residual gas analyzers for ultrahigh vacuum applications

    SciTech Connect

    M. Rao; D. Dong

    1996-10-01

    In recent years several low cost computer controlled residual gas analyzers (RGAs) have been introduced into the market place. It would be very useful to know the performance characteristics of these RGAs in order to make an informed selection for UHV applications. The UHV applications include extreme sensitivity helium leak detection and monitoring of the residual gas spectra in UHV systems. In this article, the sensitivity and linearity data for nitrogen, hydrogen, and helium are presented in the pressure range 10{sup {minus}8}---10{sup {minus}1} Pa. Further, the relationships between focus voltage and ion currents, relative sensitivity, and fragmentation factor are also included. A direct comparison method is used in obtaining this data. Spinning rotor and extractor gauges are the transfer standard gauges used in Jefferson Lab's vacuum calibration facility, with which all the reported measurements here were carried out.

  3. Isolation of TIR and non-TIR NBS--LRR resistance gene analogues and identification of molecular markers linked to a powdery mildew resistance locus in chestnut rose (Rosa roxburghii Tratt).

    PubMed

    Xu, Qiang; Wen, Xiaopeng; Deng, Xiuxin

    2005-09-01

    Toll and interleukin-1 receptor (TIR) and non-TIR nucleotide binding site-leucine rich repeat (NBS-LRR) resistance gene analogues (RGAs) were obtained from chestnut rose (Rosa roxburghii Tratt) by two PCR-based amplification strategies (direct amplification and overlap extension amplification) with degenerate primers designed to the conserved P-loop, kinase-2, and Gly-Leu-Pro-Leu (GLPL) motifs within the NBS domain of plant resistance gene (R gene) products. Thirty-four of 65 cloned PCR fragments contained a continuous open reading frame (ORF) and their predicted protein products showed homology to the NBS-LRR class R proteins in the GenBank database. These 34 predicted protein sequences exhibited a wide range (19.5--99.4%) of sequence identity among them and were classified into two distinct groups by phylogenetic analysis. The first group consisted of 23 sequences and seemed to belong to the non-TIR NBS-LRR RGAs, since they contained group specific motifs (RNBS-A-non-TIR motif) that are often present in the coiled-coil domain of the non-TIR NBS-LRR class R genes. The second group comprised 11 sequences that contained motifs found in the TIR domain of TIR NBS-LRR class R genes. Restriction fragment length polymorphic (RFLP) markers were developed from some of the RGAs and used for mapping powdery mildew resistance genes in chestnut rose. Three markers, RGA 22 C, RGA 4 A, and RGA 7 B, were identified to be linked to a resistance gene locus, designated CRPM 1 for chestnut rose powdery mildew resistance 1, which accounted for 72% of the variation in powdery mildew resistance phenotype in an F1 segregating population. To our knowledge, this is the first report on isolation, phylogenetic analysis and potential utilization as genetic markers of RGAs in chestnut rose.

  4. Highly Efficient Electronic Sensitization of Non-oxidized Graphene Flakes on Controlled Pore-loaded WO3 Nanofibers for Selective Detection of H2S Molecules

    NASA Astrophysics Data System (ADS)

    Choi, Seon–Jin; Choi, Chanyong; Kim, Sang-Joon; Cho, Hee-Jin; Hakim, Meggie; Jeon, Seokwoo; Kim, Il–Doo

    2015-01-01

    Tailoring of semiconducting metal oxide nanostructures, which possess controlled pore size and concentration, is of great value to accurately detect various volatile organic compounds in exhaled breath, which act as potential biomarkers for many health conditions. In this work, we have developed a very simple and robust route for controlling both the size and distribution of spherical pores in electrospun WO3 nanofibers (NFs) via a sacrificial templating route using polystyrene colloids with different diameters (200 nm and 500 nm). A tentacle-like structure with randomly distributed pores on the surface of electrospun WO3 NFs were achieved, which exhibited improved surface area as well as porosity. Porous WO3 NFs with enhanced surface area exhibited high gas response (Rair/Rgas = 43.1 at 5 ppm) towards small and light H2S molecules. In contrast, porous WO3 NFs with maximized pore diameter showed a high response (Rair/Rgas = 2.8 at 5 ppm) towards large and heavy acetone molecules. Further enhanced sensing performance (Rair/Rgas = 65.6 at 5 ppm H2S) was achieved by functionalizing porous WO3 NFs with 0.1 wt% non-oxidized graphene (NOGR) flakes by forming a Schottky barrier (ΔΦ = 0.11) at the junction between the WO3 NFs (Φ = 4.56 eV) and NOGR flakes (Φ = 4.67 eV), which showed high potential for the diagnosis of halitosis.

  5. Expression of resistance gene analogs in woodland strawberry (Fragaria vesca) during infection with Phytophthora cactorum.

    PubMed

    Chen, Xiao-Ren; Brurberg, May Bente; Elameen, Abdelhameed; Klemsdal, Sonja Sletner; Martinussen, Inger

    2016-10-01

    Important losses in strawberry production are often caused by the oomycete Phytophthora cactorum, the causal agent of crown rot. However, very limited studies at molecular levels exist of the mechanisms related to strawberry resistance against this pathogen. To begin to rectify this situation, a PCR-based approach (NBS profiling) was used to isolate strawberry resistance gene analogs (RGAs) with altered expression in response to P. cactorum during a time course (2, 4, 6, 24, 48, 96 and 192 h post-infection). Twenty-three distinct RGA fragments of the NB-LRR type were identified from a resistance genotype (Bukammen) of the wild species Fragaria vesca. The gene transcriptional profiles after infection showed that the response of most RGAs was quicker and stronger in the resistance genotype (Bukammen) than in the susceptible one (FDP821) during the early infection stage. The transcriptional patterns of one RGA (RGA109) were further monitored and compared during the P. cactorum infection of two pairs of resistant and susceptible genotype combinations (Bukammen/FDP821 and FDR1218/1603). The 5' end sequence was cloned, and its putative protein was characteristic of NBS-LRR R protein. Our results yielded a first insight into the strawberry RGAs responding to P. cactorum infection at molecular level.

  6. A genome-wide comparison of NB-LRR type of resistance gene analogs (RGA) in the plant kingdom.

    PubMed

    Kim, Jungeun; Lim, Chan Ju; Lee, Bong-Woo; Choi, Jae-Pil; Oh, Sang-Keun; Ahmad, Raza; Kwon, Suk-Yoon; Ahn, Jisook; Hur, Cheol-Goo

    2012-04-01

    Plants express resistance (R) genes to recognize invaders and prevent the spread of pathogens. To analyze nucleotide binding site, leucine-rich repeat (NB-LRR) genes, we constructed a fast pipeline to predict and classify the R gene analogs (RGAs) by applying in-house matrices. With predicted ~37,000 RGAs, we can directly compare RGA contents across entire plant lineages, from green algae to flowering plants. We focused on the highly divergent NBLRRs in land plants following the emergence of mosses. We identified entire loss of Toll/Interleukin-1 receptor, NBLRR (TNL) in Poaceae family of monocots and interestingly from Mimulus guttatus (a dicot), which leads to the possibility of species-specific TNL loss in other sequenced flowering plants. Using RGA maps, we have elucidated a positive correlation between the cluster sizes of NB-LRRs and their numbers. The cluster members were observed to consist of the same class of NB-LRRs or their variants, which were probably generated from a single locus for an R gene. Our website ( http://sol.kribb.re.kr/PRGA/ ), called plant resistance gene analog (PRGA), provides useful information, such as RGA annotations, tools for predicting RGAs, and analyzing domain profiles. Therefore, PRGA provides new insights into R-gene evolution and is useful in applying RGA as markers in breeding and or systematic studies.

  7. Isolation of a family of resistance gene analogue sequences of the nucleotide binding site (NBS) type from Lens species.

    PubMed

    Yaish, M W F; Sáenz de Miera, L E; Pérez de la Vega, M

    2004-08-01

    Most known plant disease-resistance genes (R genes) include in their encoded products domains such as a nucleotide-binding site (NBS) or leucine-rich repeats (LRRs). Sequences with unknown function, but encoding these conserved domains, have been defined as resistance gene analogues (RGAs). The conserved motifs within plant NBS domains make it possible to use degenerate primers and PCR to isolate RGAs. We used degenerate primers deduced from conserved motifs in the NBS domain of NBS-LRR resistance proteins to amplify genomic sequences from Lens species. Fragments from approximately 500-850 bp were obtained. The nucleotide sequence analysis of these fragments revealed 32 different RGA sequences in Lens species with a high similarity (up to 91%) to RGAs from other plants. The predicted amino acid sequences showed that lentil sequences contain all the conserved motifs (P-loop, kinase-2, kinase-3a, GLPL, and MHD) present in the majority of other known plant NBS-LRR resistance genes. Phylogenetic analyses grouped the Lens NBS sequences with the Toll and interleukin-1 receptor (TIR) subclass of NBS-LRR genes, as well as with RGA sequences isolated from other legume species. Using inverse PCR on one putative RGA of lentil, we were able to amplify the flanking regions of this sequence, which contained features found in R proteins.

  8. Expression of resistance gene analogs in woodland strawberry (Fragaria vesca) during infection with Phytophthora cactorum.

    PubMed

    Chen, Xiao-Ren; Brurberg, May Bente; Elameen, Abdelhameed; Klemsdal, Sonja Sletner; Martinussen, Inger

    2016-10-01

    Important losses in strawberry production are often caused by the oomycete Phytophthora cactorum, the causal agent of crown rot. However, very limited studies at molecular levels exist of the mechanisms related to strawberry resistance against this pathogen. To begin to rectify this situation, a PCR-based approach (NBS profiling) was used to isolate strawberry resistance gene analogs (RGAs) with altered expression in response to P. cactorum during a time course (2, 4, 6, 24, 48, 96 and 192 h post-infection). Twenty-three distinct RGA fragments of the NB-LRR type were identified from a resistance genotype (Bukammen) of the wild species Fragaria vesca. The gene transcriptional profiles after infection showed that the response of most RGAs was quicker and stronger in the resistance genotype (Bukammen) than in the susceptible one (FDP821) during the early infection stage. The transcriptional patterns of one RGA (RGA109) were further monitored and compared during the P. cactorum infection of two pairs of resistant and susceptible genotype combinations (Bukammen/FDP821 and FDR1218/1603). The 5' end sequence was cloned, and its putative protein was characteristic of NBS-LRR R protein. Our results yielded a first insight into the strawberry RGAs responding to P. cactorum infection at molecular level. PMID:27447867

  9. Identification of resistance gene analogs in Korean wild apple germplasm collections.

    PubMed

    Baek, D E; Choi, C

    2013-02-27

    Several plant disease resistance gene (R-gene) classes have been identified on the basis of specific conserved functional domains. Cloning of disease-resistance apple genes would be useful for breeding programs and for studying resistance mechanisms. We used a PCR approach with degenerate primers designed from conserved NBS-LRR (nucleotide binding site-leucine-rich repeat) regions of known R-genes to amplify and clone homologous sequences from six Korean wild apple germplasm collections and an individual plant of the Siberian wild apple, Malus baccata. One hundred and twenty-four sequenced clones showed high similarity at multiple NBS motifs with the R-genes of other plants. The clones OLE 2-9, BP 6-11, OLE 1-22, and OLE 5-13 shared 45% identity with the R-gene of other plants. The conserved sequence, which plays an important role in resistance, was found in our isolated resistance gene analogs (RGAs). The sequences of isolated apple RGAs showed more similarity to Toll/interleukin-1 receptor (TIR)-NBS-LRR than non-TIR-NBS-LRR. We suggest using a marker for this resistance gene region as well as for identifying potential material for disease-resistant breeding among Korea wild apple germplasms. This is the first step in preparing a comprehensive analysis of the RGAs in Korean wild apple germplasm.

  10. Novel applications of motif-directed profiling to identify disease resistance genes in plants

    PubMed Central

    2013-01-01

    Background Molecular profiling of gene families is a versatile tool to study diversity between individual genomes in sexual crosses and germplasm. Nucleotide binding site (NBS) profiling, in particular, targets conserved nucleotide binding site-encoding sequences of resistance gene analogs (RGAs), and is widely used to identify molecular markers for disease resistance (R) genes. Results In this study, we used NBS profiling to identify genome-wide locations of RGA clusters in the genome of potato clone RH. Positions of RGAs in the potato RH and DM genomes that were generated using profiling and genome sequencing, respectively, were compared. Largely overlapping results, but also interesting discrepancies, were found. Due to the clustering of RGAs, several parts of the genome are overexposed while others remain underexposed using NBS profiling. It is shown how the profiling of other gene families, i.e. protein kinases and different protein domain-coding sequences (i.e., TIR), can be used to achieve a better marker distribution. The power of profiling techniques is further illustrated using RGA cluster-directed profiling in a population of Solanum berthaultii. Multiple different paralogous RGAs within the Rpi-ber cluster could be genetically distinguished. Finally, an adaptation of the profiling protocol was made that allowed the parallel sequencing of profiling fragments using next generation sequencing. The types of RGAs that were tagged in this next-generation profiling approach largely overlapped with classical gel-based profiling. As a potential application of next-generation profiling, we showed how the R gene family associated with late blight resistance in the SH*RH population could be identified using a bulked segregant approach. Conclusions In this study, we provide a comprehensive overview of previously described and novel profiling primers and their genomic targets in potato through genetic mapping and comparative genomics. Furthermore, it is shown how

  11. Highly Efficient Electronic Sensitization of Non-oxidized Graphene Flakes on Controlled Pore-loaded WO3 Nanofibers for Selective Detection of H2S Molecules

    PubMed Central

    Choi, Seon–Jin; Choi, Chanyong; Kim, Sang-Joon; Cho, Hee-Jin; Hakim, Meggie; Jeon, Seokwoo; Kim, Il–Doo

    2015-01-01

    Tailoring of semiconducting metal oxide nanostructures, which possess controlled pore size and concentration, is of great value to accurately detect various volatile organic compounds in exhaled breath, which act as potential biomarkers for many health conditions. In this work, we have developed a very simple and robust route for controlling both the size and distribution of spherical pores in electrospun WO3 nanofibers (NFs) via a sacrificial templating route using polystyrene colloids with different diameters (200 nm and 500 nm). A tentacle-like structure with randomly distributed pores on the surface of electrospun WO3 NFs were achieved, which exhibited improved surface area as well as porosity. Porous WO3 NFs with enhanced surface area exhibited high gas response (Rair/Rgas = 43.1 at 5 ppm) towards small and light H2S molecules. In contrast, porous WO3 NFs with maximized pore diameter showed a high response (Rair/Rgas = 2.8 at 5 ppm) towards large and heavy acetone molecules. Further enhanced sensing performance (Rair/Rgas = 65.6 at 5 ppm H2S) was achieved by functionalizing porous WO3 NFs with 0.1 wt% non-oxidized graphene (NOGR) flakes by forming a Schottky barrier (ΔΦ = 0.11) at the junction between the WO3 NFs (Φ = 4.56 eV) and NOGR flakes (Φ = 4.67 eV), which showed high potential for the diagnosis of halitosis. PMID:25626399

  12. Parallelization of Lower-Upper Symmetric Gauss-Seidel Method for Chemically Reacting Flow

    NASA Technical Reports Server (NTRS)

    Yoon, Seokkwan; Jost, Gabriele; Chang, Sherry

    2005-01-01

    Development of technologies for exploration of the solar system has revived an interest in computational simulation of chemically reacting flows since planetary probe vehicles exhibit non-equilibrium phenomena during the atmospheric entry of a planet or a moon as well as the reentry to the Earth. Stability in combustion is essential for new propulsion systems. Numerical solution of real-gas flows often increases computational work by an order-of-magnitude compared to perfect gas flow partly because of the increased complexity of equations to solve. Recently, as part of Project Columbia, NASA has integrated a cluster of interconnected SGI Altix systems to provide a ten-fold increase in current supercomputing capacity that includes an SGI Origin system. Both the new and existing machines are based on cache coherent non-uniform memory access architecture. Lower-Upper Symmetric Gauss-Seidel (LU-SGS) relaxation method has been implemented into both perfect and real gas flow codes including Real-Gas Aerodynamic Simulator (RGAS). However, the vectorized RGAS code runs inefficiently on cache-based shared-memory machines such as SGI system. Parallelization of a Gauss-Seidel method is nontrivial due to its sequential nature. The LU-SGS method has been vectorized on an oblique plane in INS3D-LU code that has been one of the base codes for NAS Parallel benchmarks. The oblique plane has been called a hyperplane by computer scientists. It is straightforward to parallelize a Gauss-Seidel method by partitioning the hyperplanes once they are formed. Another way of parallelization is to schedule processors like a pipeline using software. Both hyperplane and pipeline methods have been implemented using openMP directives. The present paper reports the performance of the parallelized RGAS code on SGI Origin and Altix systems.

  13. The modification of residual gas analyzers to produce mass-selected ion beams

    SciTech Connect

    Gilbert, J.R.

    1990-01-01

    The authors have constructed an instrument designed to trap mass-selected ions at low temperatures within a solid inert gas matrix for spectroscopic analysis. The goal was to construct a flexible instrument that would permit the study of a wide variety of mass-selected positive ions, and which could also be used to investigate the role that counterions play in the effective trapping of ionic species in inert cryogenic hosts. The instrument was designed to utilize both laser-induced fluorescence (LIF) and Fourier transform infrared (FTIR) spectroscopies to identify and investigate the structure of the trapped species. The sources employed in this experiment must produce high current ion beams for extended periods to allow the accumulation of a significant number of absorbers in the optical beam for FTIR investigation. Residual gas analyzers (RGAs) were selected as the basis for the mass-selected ion sources for this instrument. This dissertation focuses on the modification of two RGAs to produce controlled beams of mass-selected positive and negative ions that can be directed onto a remote surface for matrix isolation experiments. The discussion includes descriptions of the modifications made to the RGA ion sources and to a commercially available chemical ionization source to produce ions by surface emission, chemical ionization, and negative surface ionization. The mass-selected beams produced by the RGA quadrupoles were focused and deflected using a series of electrostatic optics. The design of these elements was optimized using computer modeling and ion beam visualization techniques. The modifications have allowed these RGAs to produce mass-selected ion beams that have been effectively used in the isolation of mass-selected ions within solid inert gas matrices.

  14. First Wall and Operational Diagnostics

    SciTech Connect

    Lasnier, C; Allen, S; Boedo, J; Groth, M; Brooks, N; McLean, A; LaBombard, B; Sharpe, J; Skinner, C; Whyte, D; Rudakov, D; West, W; Wong, C

    2006-06-19

    In this chapter we review numerous diagnostics capable of measurements at or near the first wall, many of which contribute information useful for safe operation of a tokamak. There are sections discussing infrared cameras, visible and VUV cameras, pressure gauges and RGAs, Langmuir probes, thermocouples, and erosion and deposition measurements by insertable probes and quartz microbalance. Also discussed are dust measurements by electrostatic detectors, laser scattering, visible and IR cameras, and manual collection of samples after machine opening. In each case the diagnostic is discussed with a view toward application to a burning plasma machine such as ITER.

  15. Characterization and mapping of NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.).

    PubMed

    Soriano, J M; Vilanova, S; Romero, C; Llácer, G; Badenes, M L

    2005-03-01

    Genomic DNA sequences sharing homology with the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance genes were isolated and cloned from apricot (Prunus armeniaca L.) using a PCR approach with degenerate primers designed from conserved regions of the NBS domain. Restriction digestion and sequence analyses of the amplified fragments led to the identification of 43 unique amino acid sequences grouped into six families of resistance gene analogs (RGAs). All of the RGAs identified belong to the Toll-Interleukin receptor (TIR) group of the plant disease resistance genes (R-genes). RGA-specific primers based on non-conserved regions of the NBS domain were developed from the consensus sequences of each RGA family. These primers were used to develop amplified fragment length polymorphism (AFLP)-RGA markers by means of an AFLP-modified procedure where one standard primer is substituted by an RGA-specific primer. Using this method, 27 polymorphic markers, six of which shared homology with the TIR class of the NBS-LRR R-genes, were obtained from 17 different primer combinations. Of these 27 markers, 16 mapped in an apricot genetic map previously constructed from the self-pollination of the cultivar Lito. The development of AFLP-RGA markers may prove to be useful for marker-assisted selection and map-based cloning of R-genes in apricot.

  16. Screening and characterization of molecules that modulate the biological activity of IFNs-I.

    PubMed

    Bürgi, Milagros; Zapol'skii, Viktor A; Hinkelmann, Bettina; Köster, Mario; Kaufmann, Dieter E; Sasse, Florenz; Hauser, Hansjörg; Etcheverrigaray, Marina; Kratje, Ricardo; Bollati-Fogolín, Mariela; Oggero, Marcos

    2016-09-10

    Type I Interferons (IFNs-I) are species-specific glycoproteins which play an important role as primary defence against viral infections and that can also modulate the adaptive immune system. In some autoimmune diseases, interferons (IFNs) are over-produced. IFNs are widely used as biopharmaceuticals for a variety of cancer indications, chronic viral diseases, and for their immuno-modulatory action in patients with multiple sclerosis; therefore, increasing their therapeutic efficiency and decreasing their side effects is of high clinical value. In this sense, it is interesting to find molecules that can modulate the activity of IFNs. In order to achieve that, it was necessary to establish a simple, fast and robust assay to analyze numerous compounds simultaneously. We developed four reporter gene assays (RGAs) to identify IFN activity modulator compounds by using WISH-Mx2/EGFP, HeLa-Mx2/EGFP, A549-Mx2/EGFP, and HEp2-Mx2/EGFP reporter cell lines (RCLs). All of them present a Z' factor higher than 0.7. By using these RGAs, natural and synthetic compounds were analyzed simultaneously. A total of 442 compounds were studied by the Low Throughput Screening (LTS) assay using the four RCLs to discriminate between their inhibitory or enhancing effects on IFN activity. Some of them were characterized and 15 leads were identified. Finally, one promising candidate with enhancing effect on IFN-α/-β activity and five compounds with inhibitory effect were described.

  17. Development and linkage mapping of E-STS and RGA markers for functional gene homologues in apple.

    PubMed

    Naik, Suresh; Hampson, Cheryl; Gasic, Ksenija; Bakkeren, Guus; Korban, Schuyler S

    2006-08-01

    Linkage maps developed from known-function genes can be valuable in the candidate gene mapping approach. A set of 121 expressed sequence tagged site (E-STS) primer pairs were tested on a framework genetic linkage map of apple (Malus x domestica Borkh.) constructed using simple sequence repeats (SSRs) and randomly amplified polymorphic DNA (RAPD) markers. These known-function gene markers, E-STSs, were supplemented by markers for resistance gene analogues (RGAs), designed based on conserved motifs in all characterized resistance genes isolated from plant species. A total of 229 markers, including 46 apple E-STSs, 8 RGAs, 85 SSRs from apple and peach, and 88 RAPDs, were assigned to 17 linkage groups covering 832 cM of the apple genome, based on 52 individuals originating from the cross 'Antonovka debnicka' (Q12-4) x 'Summerred'. Clusters of E-STS and RGA loci were located in linkage groups previously identified to carry resistance genes, some of which confer resistance to apple scab disease caused by Venturia inaequalis (Cke.) Wint.

  18. Facile Au catalyst loading on the inner shell of hollow SnO2 spheres using Au-decorated block copolymer sphere templates and their selective H2S sensing characteristics.

    PubMed

    Choi, Seon-Jin; Kim, Minsoo P; Lee, Seo-Jin; Kim, Bumjoon J; Kim, Il-Doo

    2014-10-21

    Hollow SnO2 spheres functionalized by Au catalysts were synthesized via the use of Au-decorated block copolymer (Au-BCP) sphere templates. Uniformly distributed Au nanoparticles on BCP spheres were prepared by the infiltration of Au precursors into polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) spheres. A thin SnO2 layer was coated on the Au-BCP spheres using RF sputtering at room temperature without morphological deformation of the spheres. The Au nanoparticles were uniformly transferred from the Au-BCP spheres to the inner shells of the hollow SnO2 spheres followed by decomposition of BCP spheres. The Au-loaded hollow SnO2 spheres exhibited a superior H2S sensitivity (Rair/Rgas = 17.4 at 5 ppm) with remarkably selective characteristics with a minor response (Rair/Rgas < 2.5 at 5 ppm) toward other interfering gases. Our results pave the way for a new catalyst loading method using Au-BCP spheres for the uniformly distributed Au NPs on the SnO2 layers. PMID:25175492

  19. Great Plains ASPEN model development: gasifier model. Final topical report

    SciTech Connect

    Benjamin, B.W.

    1985-01-01

    A rigorous model of a moving-bed, dry-bottom gasifier, RGAS, has been incorporated into ASPEN. The model is designed to calculate the variables which characterize gasifier performance: (1) the composition of the outlet gas; (2) the flow of the outlet gas; (3) the temperature of the outlet gas; (4) the temperature profile of the solids (especially important in dry bottom gasifiers because of the necessity of maintaining the maximum temperature of the bed below the ash softening temperature); and (5) the rate of steam generation in the jacket (if applicable). The option of using alternative kinetic expressions has been incorporated into the model structure. Presently, RGAS can be used to simulate gasifier performance using the kinetic expressions for gasification established at West Virginia University and the University of Delaware. The models of both West Virginia University and the University of Delaware were tuned to agree with the Great Plains gasifier flowsheet. Then, several case studies were run to determine the sensitivity of each model to changes in such inputs as: (1) feed rates; (2) feed temperatures; (3) reaction parameters; and (4) heat transfer coefficient. The data from these case studies have been compared with experimental findings. For example, increasing the oxygen feed rate or increasing the temperature of the inlet gas feed both serve to increase the reactor temperature which, in turn, increases the carbon conversion and steam generation rate. On the other hand, increasing the steam feed rate does the opposite. These results agree with trends observed experimentally. 5 references.

  20. Ag-doped titanium dioxide gas sensor

    NASA Astrophysics Data System (ADS)

    Alaei Sheini, Navid; Rohani, Mahsa

    2016-03-01

    Titanium dioxide has been utilized for the fabrication of oxygen sensitive ceramic bodies. In this work, disk-shaped TiO2 pellets are fabricated by the sintering of the press- formed anatase powder at 1000°C. Two silver contacts are printed on one of the top base of each sample. Silver wire segments are connected to the printed electrodes. It is shown that the gradual diffusion of silver into titanium dioxide from the electrodes profoundly affects the resistive properties of the ceramic samples. SEM, XRD and EDAX analyses are carried out to determine the position of the silver diffused in the structure. At 35°C, before silver diffusion, the electrical resistance of the device decreases ten times in response to the presence of 3000 ppm ethanol contamination. Sensitivity (Rair/Rgas) to reducing gases is severely affected by the silver doping level in the titanium dioxide. The progress of silver diffusion continuously decreases the sensitivity till it become less than one. Further progress in silver diffusion brings the devices to the condition at which the resistance increases at the presents of reducing gases. In this condition, inverse sensitivities (Rgas/Rair) as large as 103 are demonstrated.

  1. Identification and characterization of novel NBS-LRR resistance gene analogues from the pea.

    PubMed

    Djebbi, S; Bouktila, D; Makni, H; Makni, M; Mezghani-Khemakhem, M

    2015-01-01

    Pea (Pisum sativum) is one of the most cultivated le-gumes in the world, and its yield and seed quality are affected by a variety of pathogens. In plants, NBS-LRR (nucleotide binding site-leucine-rich repeat) is the main class of disease resistance genes. Using degenerate primers deduced from conserved motifs in the NBS domain of known resistance genes, we identified 10 NBS sequences in three varieties of P. sativum. The deduced amino acid sequences of the iden-tified resistance gene analogues (RGAs) exhibited the typical motifs of the NBS domain (P-loop, kinase-2, kinase-3a, and the hydrophobic domain, GLPL) present in the majority of plant proteins belonging to the NBS-LRR class. Phylogenetic analysis showed that seven RGAs belonged to the non-TIR-NBS-LRR subclass and three to the TIR-NBS-LRR subclass. The results of this study provide insights into the structure of this class of resistance genes in the pea, and their evolution-ary relationships with those of other plant species.

  2. An investigation of the endocrine disrupting potential of enniatin B using in vitro bioassays.

    PubMed

    Kalayou, Shewit; Ndossi, Doreen; Frizzell, Caroline; Groseth, Per Kristian; Connolly, Lisa; Sørlie, Morten; Verhaegen, Steven; Ropstad, Erik

    2015-03-01

    Evidence that some of the fungal metabolites present in food and feed may act as potential endocrine disruptors is increasing. Enniatin B (ENN B) is among the emerging Fusarium mycotoxins known to contaminate cereals. In this study, the H295R and neonatal porcine Leydig cell (LC) models, and reporter gene assays (RGAs) have been used to investigate the endocrine disrupting activity of ENN B. Aspects of cell viability, cell cycle distribution, hormone production as well as the expression of key steroidogenic genes were assessed using the H295R cell model. Cell viability and hormone production levels were determined in the LC model, while cell viability and steroid hormone nuclear receptor transcriptional activity were measured using the RGAs. ENN B (0.01-100μM) was cytotoxic in the H295R and LC models used; following 48h incubation with 100μM. Flow cytometry analysis showed that ENN B exposure (0.1-25μM) led to an increased proportion of cells in the S phase at higher ENN B doses (>10μM) while cells at G0/G1 phase were reduced. At the receptor level, ENN B (0.00156-15.6μM) did not appear to induce any specific (ant) agonistic responses in reporter gene assays (RGAs), however cell viability was affected at 15.6μM. Measurement of hormone levels in H295R cells revealed that the production of progesterone, testosterone and cortisol in exposed cells were reduced, but the level of estradiol was not significantly affected. There was a general reduction of estradiol and testosterone levels in exposed LC. Only the highest dose (100μM) used had a significant effect, suggesting the observed inhibitory effect is more likely associated with the cytotoxic effect observed at this dose. Gene transcription analysis in H295R cells showed that twelve of the sixteen genes were significantly modulated (p<0.05) by ENN B (10μM) compared to the control. Genes HMGR, StAR, CYP11A, 3βHSD2 and CYP17 were downregulated, whereas the expression of CYP1A1, NR0B1, MC2R, CYP21, CYP11B1, CYP

  3. Mesoporous WO3 Nanofibers with Protein-Templated Nanoscale Catalysts for Detection of Trace Biomarkers in Exhaled Breath.

    PubMed

    Kim, Sang-Joon; Choi, Seon-Jin; Jang, Ji-Soo; Kim, Nam-Hoon; Hakim, Meggie; Tuller, Harry L; Kim, Il-Doo

    2016-06-28

    Highly selective detection, rapid response (<20 s), and superior sensitivity (Rair/Rgas> 50) against specific target gases, particularly at the 1 ppm level, still remain considerable challenges in gas sensor applications. We propose a rational design and facile synthesis concept for achieving exceptionally sensitive and selective detection of trace target biomarkers in exhaled human breath using a protein nanocage templating route for sensitizing electrospun nanofibers (NFs). The mesoporous WO3 NFs, functionalized with well-dispersed nanoscale Pt, Pd, and Rh catalytic nanoparticles (NPs), exhibit excellent sensing performance, even at parts per billion level concentrations of gases in a humid atmosphere. Functionalized WO3 NFs with nanoscale catalysts are demonstrated to show great promise for the reliable diagnosis of diseases. PMID:27166639

  4. Graphic Three-Axes Presentation of Residual Gas Analyser Data

    NASA Technical Reports Server (NTRS)

    Johnson, Kenneth R.; Levi, Alejandro G.

    1996-01-01

    Residual gas analyzers (RGA) are commonly used to measure the composition of residual gases in thermal-vacuum test chambers. Measurements from RGAs are often used to identify and quantify outgassing contaminants from a test article during thermal-vacuum testing. RGA data is typically displayed as snapshots in time, showing instantaneous concentrations of ions from ionized residual gas molecules at different atomic masses. A method was devised by the authors to present RGA data in a three-axis format, plotting atomic mass unit (AMU), ion concentration as a function of AMU, and time, to provide a clear graphic visualization ot trends in gas concentration changes and to initiate a valuable analytical tool to interpret test article outgassing rates during thermal-vacuum testing.

  5. Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci.

    PubMed

    Urso, Simona; Desiderio, Francesca; Biselli, Chiara; Bagnaresi, Paolo; Crispino, Laura; Piffanelli, Pietro; Abbruscato, Pamela; Assenza, Federica; Guarnieri, Giada; Cattivelli, Luigi; Valè, Giampiero

    2016-02-01

    Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30 % of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78 % of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.

  6. Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz).

    PubMed

    Tomkins, J; Fregene, M; Main, D; Kim, H; Wing, R; Tohme, J

    2004-11-01

    Pest and disease problems are important constraints of cassava production and host plant resistance is the most efficient method of combating them. Breeding for host plant resistance is considerably slowed down by the crop's biological constraints of a long growth cycle, high levels of heterozygosity and a large genetic load. More efficient methods such as gene cloning and transgenesis are required to deploy resistance genes. To facilitate the cloning of resistance genes, bacterial artificial chromosome (BAC) library resources have been developed for cassava. Two libraries were constructed from the cassava clones, TMS 30001, resistant to the cassava mosaic disease (CMD) and the cassava bacterial blight (CBB), and MECU72, resistant to cassava white fly. The TMS30001 library has 55, 296 clones with an insert size range of 40-150 kb with an average of 80 kb, while the MECU72 library consists of 92 160 clones and an insert size range of 25-250 kb average of 93 kb. Based on a genome size of 772 Mb, the TMS30001 and MECU72 libraries have a 5 and 11.3 haploid genome equivalents and a 95 and 99 chance of finding any sequence, respectively. To demonstrate the potential of the libraries, the TMS30001 library was screened by southern hybridization using a cassava analog (CBB1) of the Xa21 gene from rice that maps to a region containing a QTL for resistance to CBB as probe. Five BAC clones that hybridized to CBB1 were isolated and a Hind III fingerprint revealed 2-3 copies of the gene in individual BAC clones. A larger scale analysis of resistance gene analogs (RGAs) in cassava has also been conducted in order to understand the number and organization of RGAs. To scan for gene and repeat DNA content in the libraries, end-sequencing was performed on 2,301 clones from the MECU72 library. A total of 1705 unique sequences were obtained with an average size of 715 bp. Database homology searches using BLAST revealed that 458 sequences had significant homology with known proteins and

  7. Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats.

    PubMed

    Sanz, M J; Loarce, Y; Fominaya, A; Vossen, J H; Ferrer, E

    2013-01-01

    Two of the domains most widely shared among R genes are the nucleotide binding site (NBS) and protein kinase (PK) domains. The present study describes and maps a number of new oat resistance gene analogues (RGAs) with two purposes in mind: (1) to identify genetic regions that contain R genes and (2) to determine whether RGAs can be used as molecular markers for qualitative loci and for QTLs affording resistance to Puccinia coronata. Such genes have been mapped in the diploid A. strigosa × A. wiestii (Asw map) and the hexaploid MN841801-1 × Noble-2 (MN map). Genomic and cDNA NBS-RGA probes from oat, barley and wheat were used to produce RFLPs and to obtain markers by motif-directed profiling based on the NBS (NBS profiling) and PK (PK profiling) domains. The efficiency of primers used in NBS/PK profiling to amplify RGA fragments was assessed by sequencing individual marker bands derived from genomic and cDNA fragments. The positions of 184 markers were identified in the Asw map, while those for 99 were identified in the MN map. Large numbers of NBS and PK profiling markers were found in clusters across different linkage groups, with the PK profiling markers more evenly distributed. The location of markers throughout the genetic maps and the composition of marker clusters indicate that NBS- and PK-based markers cover partly complementary regions of oat genomes. Markers of the different classes obtained were found associated with the two resistance loci, PcA and R-284B-2, mapped on Asw, and with five out of eight QTLs for partial resistance in the MN map. 53 RGA-RFLPs and 187 NBS/PK profiling markers were also mapped on the hexaploid map A. byzantina cv. Kanota × A. sativa cv. Ogle. Significant co-localization was seen between the RGA markers in the KO map and other markers closely linked to resistance loci, such as those for P. coronata and barley yellow dwarf virus (Bydv) that were previously mapped in other segregating populations.

  8. Multi-Objective Optimization of Transmission Lines / Elektropārvades Līnijas Daudzkriteriālā Optimizācija

    NASA Astrophysics Data System (ADS)

    Berjozkina, S.; Sauhats, A.; Neimane, V.

    2013-10-01

    Introduction of new advanced electrical connections into a transmission grid reduces the capacity of existing overhead lines (OHLs). At the same time, designing & building of new OHLs and substations involves considerable technical, environmental and economical problems. The authors propose a concept of the multi-objective optimization for selection of transmission line routes, towers (their type, placement and geometry), of conductors, insulators, dampers, earthing and lightning protection systems, span lengths, etc.. The optimization is organized in five stages. At the first and second stages a search for optimum solutions is performed along with determination of the main impacting factors. The next two stages present a two-objective optimization based on Pareto's approach. At the last stage (exemplified by a case study), the probability of the restriction removal conditions is assessed, and preventive measures are identified. The presented approach uses a real line design and is intended for minimizing the total invested capital and maximizing the net present value. In the framework of this approach 20 alternatives have been elaborated, which can successfully be applied in the cases described in the paper. Elektropārvades tīklam rodas nepieciešamība pēc jauniem elektriskajiem pieslēgumiem, kas noved pie esošo gaisvadu līniju jaudas nepietiekamības. Viens no iespējamajiem pastāvošās problēmas risinājumiem ir jaunu gaisvadu līniju un apakšstacijas būvniecība. Gaisvadu līniju projektēšana ir saistīta ar ievērojamām tehniskām, vides un ekonomiskām problēmām. Darbā aprakstīta elektropārvades līnijas optimālās trases izvēles daudzkritēriju optimizācijas koncepcija, ieskaitot balstu tipa, balstu izvietojuma koordināšu, balstu ģeometrijas, vadu tipu un parametru, izolatoru tipu, vibroslāpētāju tipu, zibensaizsardzības un zemēšanas sistēmu, kā arī laidumu garumu izvēles optimizāciju. Optimizācijas uzdevums tiek organiz

  9. Removal of natural hormones in dairy farm wastewater using reactive and sorptive materials.

    PubMed

    Cai, Kai; Phillips, Debra H; Elliott, Christopher T; Muller, Marc; Scippo, Marie-Louise; Connolly, Lisa

    2013-09-01

    The objective of this study was to examine the oestrogen and androgen hormone removal efficiency of reactive (Connelly zero-valent iron (ZVI), Gotthart Maier ZVI) and sorptive (AquaSorb 101 granular activated carbon (GAC) and OrganoLoc PM-100 organoclay (OC)) materials from HPLC grade water and constructed wetland system (CWS) treated dairy farm wastewater. Batch test studies were performed and hormone concentration analysis carried out using highly sensitive reporter gene assays (RGAs). The results showed that hormonal interaction with these materials is selective for individual classes of hormones. Connelly ZVI and AquaSorb 101 GAC were more efficient in removing testosterone (Te) than 17β-estradiol (E2) and showed faster removal rates of oestrogen and androgen than the other materials. Gotthart Maier ZVI was more efficient in removing E2 than Te. OrganoLoc PM-100 OC achieved the lowest final concentration of E2 equivalent (EEQ) and provided maximum removal of both oestrogens and androgens. PMID:23712110

  10. Electrosprayed Metal Oxide Semiconductor Films for Sensitive and Selective Detection of Hydrogen Sulfide

    PubMed Central

    Ghimbeu, Camelia Matei; Lumbreras, Martine; Schoonman, Joop; Siadat, Maryam

    2009-01-01

    Semiconductor metal oxide films of copper-doped tin oxide (Cu-SnO2), tungsten oxide (WO3) and indium oxide (In2O3) were deposited on a platinum coated alumina substrate employing the electrostatic spray deposition technique (ESD). The morphology studied with scanning electron microscopy (SEM) and atomic force microscopy (AFM) shows porous homogeneous films comprising uniformly distributed aggregates of nano particles. The X-ray diffraction technique (XRD) proves the formation of crystalline phases with no impurities. Besides, the Raman cartographies provided information about the structural homogeneity. Some of the films are highly sensitive to low concentrations of H2S (10 ppm) at low operating temperatures (100 and 200 °C) and the best response in terms of Rair/Rgas is given by Cu-SnO2 films (2500) followed by WO3 (1200) and In2O3 (75). Moreover, all the films exhibit no cross-sensitivity to other reducing (SO2) or oxidizing (NO2) gases. PMID:22291557

  11. Optimization of flight control parameters of an aircraft using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Garcia Aguilar, Sixto Ernesto

    Ce travail presente de nouvelles methodes pour ameliorer la performance des algorithmes genetiques pour l'optimisation des gains du controleur d'un systeme de vol electrique des avions commerciaux. Nous avons combine les caracteristiques de deux operateurs de mutation, uniforme et non uniforme, au sein d'un nouvel operateur, de type periodique. Nous avons propose un nouveau modele avec contraintes et nous avons fait la conception d'un nouvel operateur de selection stochastique pour augmenter l'efficacite d'un algorithme genetique du codage reel (RGA) applique aux problemes d'optimisation avec contraintes. Pour la conception de l'operateur de selection sous contraintes, nous avons applique une methode qui peut manipuler la proportion d'individus faisables et non faisables sans negliger le comportement dynamique du GA. Finalement, nous avons reduit de 25% le temps d'execution original et ameliore l'efficacite des RGAs en combinant l'application d'un index de diversite d'une population d'un algorithme genetique ainsi qu'un reseau de Bayes (BN).

  12. Estrogenic endocrine disruptors present in sports supplements. A risk assessment for human health.

    PubMed

    Plotan, Monika; Elliott, Christopher T; Frizzell, Caroline; Connolly, Lisa

    2014-09-15

    Sports supplements are becoming a regular dietary addition for consumers who view such products as a means of improving their health and performance. Previously estrogenic endocrine disruptors (EDs) were detected in 80% of 116 sports supplements investigated by biological in vitro reporter gene assays (RGAs). The aim of this study was to quantify the hormonal activity in 50 of these sports supplement samples using a validated estrogen RGA and perform an exposure and risk assessment for human health. Results showed that 17β-estradiol equivalent levels were higher than those reported as being present in the typical human omnivore diet in 33 of the sports supplements and higher than the acceptable daily intake (ADI) in 13 of these products. The highest activity samples presented a potential to influence the human daily exposure to 17β-estradiol like activity in various risk groups with a predicted hormonal impact of greatest concern in young boys and postmenopausal women. In conclusion, consumers of sports supplements may be exposed to high levels of estrogenic EDs.

  13. Removal of natural hormones in dairy farm wastewater using reactive and sorptive materials.

    PubMed

    Cai, Kai; Phillips, Debra H; Elliott, Christopher T; Muller, Marc; Scippo, Marie-Louise; Connolly, Lisa

    2013-09-01

    The objective of this study was to examine the oestrogen and androgen hormone removal efficiency of reactive (Connelly zero-valent iron (ZVI), Gotthart Maier ZVI) and sorptive (AquaSorb 101 granular activated carbon (GAC) and OrganoLoc PM-100 organoclay (OC)) materials from HPLC grade water and constructed wetland system (CWS) treated dairy farm wastewater. Batch test studies were performed and hormone concentration analysis carried out using highly sensitive reporter gene assays (RGAs). The results showed that hormonal interaction with these materials is selective for individual classes of hormones. Connelly ZVI and AquaSorb 101 GAC were more efficient in removing testosterone (Te) than 17β-estradiol (E2) and showed faster removal rates of oestrogen and androgen than the other materials. Gotthart Maier ZVI was more efficient in removing E2 than Te. OrganoLoc PM-100 OC achieved the lowest final concentration of E2 equivalent (EEQ) and provided maximum removal of both oestrogens and androgens.

  14. User's guide to the Residual Gas Analyzer (RGA)

    SciTech Connect

    Artman, S.A.

    1988-08-04

    The Residual Gas Analyzer (RGA), a Model 100C UTI quadrupole mass spectrometer, measures the concentrations of selected masses in the Fusion Energy Division's (FED) Advanced Toroidal Facility (ATF). The RGA software is a VAX FORTRAN computer program which controls the experimental apparatus, records the raw data, performs data reduction, and plots the data. The RGA program allows data to be collected from an RGA on ATF or from either of two RGAs in the laboratory. In the laboratory, the RGA diagnostic plays an important role in outgassing studied on various candidate materials for fusion experiments. One such material, graphite, is being used more often in fusion experiments due to its ability to withstand high power loads. One of the functions of the RGA diagnostic is aid in the determination of the best grade of graphite to be used in these experiments and to study the procedures used to condition it. A procedure of particular interest involves baking the graphite sample in order to remove impurities that may be present in it. These impurities can be studied while in the ATF plasma or while being baked and outgassed in the laboratory. The Residual Gas Analyzer is a quadrupole mass spectrometer capable of scanning masses ranging in size from 1 atomic mass unit (amu) to 300 amu while under computer control. The procedure for collecting data for a particular mass is outlined.

  15. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    PubMed

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana.

  16. In vitro bioassay investigations of the endocrine disrupting potential of steviol glycosides and their metabolite steviol, components of the natural sweetener Stevia.

    PubMed

    Shannon, Maeve; Rehfeld, Anders; Frizzell, Caroline; Livingstone, Christina; McGonagle, Caoimhe; Skakkebaek, Niels E; Wielogórska, Ewa; Connolly, Lisa

    2016-05-15

    The food industry is moving towards the use of natural sweeteners such as those produced by Stevia rebaudiana due to the number of health and safety concerns surrounding artificial sweeteners. Despite the fact that these sweeteners are natural; they cannot be assumed safe. Steviol glycosides have a steroidal structure and therefore may have the potential to act as an endocrine disruptor in the body. Reporter gene assays (RGAs), H295R steroidogenesis assay and Ca(2+) fluorimetry based assays using human sperm cells have been used to assess the endocrine disrupting potential of two steviol glycosides: stevioside and rebaudioside A, and their metabolite steviol. A decrease in transcriptional activity of the progestagen receptor was seen following treatment with 25,000 ng/ml steviol in the presence of progesterone (157 ng/ml) resulting in a 31% decrease in progestagen response (p=<0.01). At the level of steroidogenesis, the metabolite steviol (500-25,000 ng/ml) increased progesterone production significantly by 2.3 fold when exposed to 10,000 ng/ml (p=<0.05) and 5 fold when exposed to 25,000 ng/ml (p=<0.001). Additionally, steviol was found to induce an agonistic response on CatSper, a progesterone receptor of sperm, causing a rapid influx of Ca(2+). The response was fully inhibited using a specific CatSper inhibitor. These findings highlight the potential for steviol to act as a potential endocrine disruptor. PMID:26965840

  17. A hydrogen ion beam method of molecular density measurement inside a 4.2-K beam tube

    SciTech Connect

    Alinovsky, N.; Anashin, V.; Beschasny, P.

    1994-06-01

    In our first experiments on synchrotron radiation-induced photodesorption in a 4.2-K beam tube, the moleculm density was measured by room temperature ion gauges and RGAs outside the beam tube. The molecular density inside the 4.2-K beam tube was therefore unknown, since the mean molecular speed of photodesorbed molecules had not been measured. To determine the density inside the 4.2-K beam tube we have developed a direct method of measurement utilizing the neutralization of H{sup +} beams, which are proportional to gas density. The hydrogen ion beams (up to 20 keV, {approximately}1 {mu}A) are extracted from an rf ion source and guided into the cold beam tube by a bending magnet. The H{sup 0} and H{sup {minus}} produced in the beam tube are magnetically separated from H{sup {minus}} and detected with secondary electron multipliers (SEMs). Small superconducting dipole magnets located near the center of the beam tube allow a {approximately}20-cm segment of the injected ion beam to be offset a few mm from the injection axis; detection of H{sup 0} and H{sup {minus}} produced along this offset segment provides a localized density measurement. If necessary, detector background due to synchrotron radiation photons can be discriminated against by gating the detector on between the bursts of synchrotron radiation. The experimental setup and initial data will be presented.

  18. Remote geologic structural analysis of Yucca Flat

    SciTech Connect

    Foley, M.G.; Heasler, P.G.; Hoover, K.A.; Rynes, N.J.; Thiessen, R.L.; Alfaro, J.L.

    1991-12-01

    The Remote Geologic Analysis (RGA) system was developed by Pacific Northwest Laboratory (PNL) to identify crustal structures that may affect seismic wave propagation from nuclear tests. Using automated methods, the RGA system identifies all valleys in a digital elevation model (DEM), fits three-dimensional vectors to valley bottoms, and catalogs all potential fracture or fault planes defined by coplanar pairs of valley vectors. The system generates a cluster hierarchy of planar features having greater-than-random density that may represent areas of anomalous topography manifesting structural control of erosional drainage development. Because RGA uses computer methods to identify zones of hypothesized control of topography, ground truth using a well-characterized test site was critical in our evaluation of RGA`s characterization of inaccessible test sites for seismic verification studies. Therefore, we applied RGA to a study area centered on Yucca Flat at the Nevada Test Site (NTS) and compared our results with both mapped geology and geologic structures and with seismic yield-magnitude models. This is the final report of PNL`s RGA development project for peer review within the US Department of Energy Office of Arms Control (OAC) seismic-verification community. In this report, we discuss the Yucca Flat study area, the analytical basis of the RGA system and its application to Yucca Flat, the results of the analysis, and the relation of the analytical results to known topography, geology, and geologic structures. 41 refs., 39 figs., 2 tabs.

  19. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    PubMed

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana. PMID:24099390

  20. VizieR Online Data Catalog: Extremely strong damped Lyman-α systems (Noterdaeme+, 2014)

    NASA Astrophysics Data System (ADS)

    Noterdaeme, P.; Petitjean, P.; Paris, I.; Cai, Z.; Finley, H.; Ge, J.; Pieri, M. M.; York, D. G.

    2014-07-01

    , velocity width and velocity offset compared to systemic redshift) are very similar to that of the population of Lyman-α emitting galaxies (LAEs) with LLAE(Lyα)>=1041erg/s detected in long-slit spectroscopy or narrow-band imaging surveys. By matching the incidence of ESDLAs with that of the LAEs population, we estimate the high column density gas radius to be about rgas=2.5kpc, i.e., significantly smaller than the radius corresponding to the BOSS fibre aperture, making fibre losses likely negligible. Finally, the average measured Lyα luminosity indicates a star-formation rate consistent with the Schmidt-Kennicutt law, SFR (M⊙/yr)=~0.6/fesc, where fesc<1 is the Lyα escape fraction. Assuming the typical escape fraction of LAEs, fesc~0.3, the Schmidt-Kennicutt law implies a galaxy radius of about rgal=~2.5kpc. Finally, we note that possible overestimation of the Lyα emission would result in both smaller rgas and rgal. Our results support a close association between LAEs and strong DLA host galaxies. (1 data file).

  1. Coaxial electrospinning of WO3 nanotubes functionalized with bio-inspired Pd catalysts and their superior hydrogen sensing performance

    NASA Astrophysics Data System (ADS)

    Choi, Seon-Jin; Chattopadhyay, Saptarshi; Kim, Jae Jin; Kim, Sang-Joon; Tuller, Harry L.; Rutledge, Gregory C.; Kim, Il-Doo

    2016-04-01

    Macroporous WO3 nanotubes (NTs) functionalized with nanoscale catalysts were fabricated using coaxial electrospinning combined with sacrificial templating and protein-encapsulated catalysts. The macroporous thin-walled nanotubular structures were obtained by introducing colloidal polystyrene (PS) particles to a shell solution of W precursor and poly(vinylpyrrolidone). After coaxial electrospinning with a core liquid of mineral oil and subsequent calcination, open pores with an average diameter of 173 nm were formed on the surface of WO3 NTs due to decomposition of the PS colloids. In addition, catalytic Pd nanoparticles (NPs) were synthesized using bio-inspired protein cages, i.e., apoferritin, and uniformly dispersed within the shell solution and subsequently on the WO3 NTs. The resulting Pd functionalized macroporous WO3 NTs were demonstrated to be high performance hydrogen (H2) sensors. In particular, Pd-functionalized macroporous WO3 NTs exhibited a very high H2 response (Rair/Rgas) of 17.6 at 500 ppm with a short response time. Furthermore, the NTs were shown to be highly selective for H2 compared to other gases such as carbon monoxide (CO), ammonia (NH3), and methane (CH4). The results demonstrate a new synthetic method to prepare highly porous nanotubular structures with well-dispersed nanoscale catalysts, which can provide improved microstructures for chemical sensing.Macroporous WO3 nanotubes (NTs) functionalized with nanoscale catalysts were fabricated using coaxial electrospinning combined with sacrificial templating and protein-encapsulated catalysts. The macroporous thin-walled nanotubular structures were obtained by introducing colloidal polystyrene (PS) particles to a shell solution of W precursor and poly(vinylpyrrolidone). After coaxial electrospinning with a core liquid of mineral oil and subsequent calcination, open pores with an average diameter of 173 nm were formed on the surface of WO3 NTs due to decomposition of the PS colloids. In addition

  2. Reporter enzyme inhibitor study to aid assembly of orthogonal reporter gene assays.

    PubMed

    Ho, Pei-i; Yue, Kimberley; Pandey, Pramod; Breault, Lyne; Harbinski, Fred; McBride, Aaron J; Webb, Brian; Narahari, Janaki; Karassina, Natasha; Wood, Keith V; Hill, Adam; Auld, Douglas S

    2013-05-17

    Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and to develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (Photinus pyralis), Renilla reniformis luciferase, and β-lactamase, as well as mutated forms of R. reniformis luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of Luciola cruciata firefly luciferase, a mutated form of Gaussia princeps luciferase, and a proprietary luciferase termed "NanoLuc" derived from the luminescent sea shrimp Oplophorus gracilirostris. To determine hit rates and structure-activity relationships, we screened a collection of 42,460 PubChem compounds at 10 μM using purified enzyme preparations. We then compared hit rates and chemotypes of actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of Renilla luciferase. Related luciferases such as Renilla luciferase mutants showed high degrees of inhibitor overlap (40-70%), while unrelated luciferases such as firefly luciferases, Gaussia luciferase, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based enzyme stabilization can lead to increases in bioluminescent signal for firefly luciferase, Renilla luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these reporter enzymes.

  3. Non-TIR-NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.).

    PubMed

    Gutermuth, A; György, Zsuzsanna; Hegedus, A; Pedryc, A

    2011-06-01

    Genes encoding for proteins with nucleotide-binding site and leucine-rich repeat motifs (NBS-LRR) have been suggested to play a general role in plant defence mechanism. In Prunus species, many TIR (Toll / Interleukin-1 Receptor), and only very few non-TIR sequences were identified, which was explained either by the unequal distribution of TIR/non-TIR sequences in the Prunus genome or by the incapability of primers in the amplification of non-TIR RGAs. The objective of this work was to check whether a new semi-nested PCR strategy can be developed for the targeted isolation of non-TIR-NBS-LRR Resistance Gene Analog (RGA) sequences from apricot. Three primers (CUB-P-loop F, CUB-Kin2 F and CUB-HD R) were designed, from which CUB-Kin2 F and CUB-HD R were constructed to anneal selectively to the non-TIR sequences. A colony Polymerase Chain Reaction (PCR) indicated that out of the 96 clones tested 28 showed amplification using the newly developed primers, while no amplification occurred when using the formerly described primers. Half of the 28 positive clones were sequenced and they turned out to represent 11 different non-TIR RGA sequences. A phylogenetic analysis was carried out based on an alignment containing 293 Rosaceae and 21 non-Rosaceaa sequences. A significantly higher ratio (91%) of non-TIR sequences were arranged in multi-genera clades than that of (57%) the TIR groups confirming that non-TIR sequences might be of more ancient origin than TIR sequences.

  4. Thin-walled SnO₂ nanotubes functionalized with Pt and Au catalysts via the protein templating route and their selective detection of acetone and hydrogen sulfide molecules.

    PubMed

    Jang, Ji-Soo; Kim, Sang-Joon; Choi, Seon-Jin; Kim, Nam-Hoon; Hakim, Meggie; Rothschild, Avner; Kim, Il-Doo

    2015-10-21

    Bio-inspired Pt (∼2 nm) and Au (∼2.7 nm) catalysts encapsulated by a protein shell, i.e., Pt-apoferritin (Pt@AF) and Au-apoferriten (Au@AF), were synthesized via the hollow protein nanocage (apoferritin) templating route and directly functionalized on the interior and exterior walls of electrospun SnO2 nanotubes (NTs) during controlled single-nozzle electrospinning followed by high temperature calcination with heating rate control. Fast crystallization of the exterior shell and outward diffusion of the interior Sn precursors and crystallites result in the continued growth of a tubular wall, which is related to rapid heating driven Ostwald-ripening behavior. Very importantly, the Pt and Au nanoparticles (NPs) were immobilized onto thin-walled SnO2 NTs with a diameter of ∼350 nm and a shell thickness of ∼40 nm without any aggregation of catalysts due to high dispersibility, which originated from repulsive electrostatic (Coulombic) forces acting on the surface charged protein shells, leading to an enhanced catalytic effect and outstanding gas sensing properties. Pt-loaded SnO2 NTs exhibited superior acetone response (R(air)/R(gas) = 92 at 5 ppm) compared to pure SnO2 NFs (R(air)/R(gas) = 4.8 at 5 ppm) and SnO2 NTs (Rair/Rgas = 11 at 5 ppm) while Au-loaded SnO2 NTs showed a high response when exposed to hydrogen sulfide (R(air)/R(gas) = 34 at 5 ppm), offering selective gas detection with minimal cross-sensitivity against other interfering gases such as NH3, CO, NO, C6H5CH3, and C5H12. Our results provide a new insight into facile, cost-effective, and highly dispersible catalyst loading on the interior and exterior walls of hollow metal oxide NTs via simple electrospinning as a potential breath analyzer.

  5. Genome Mapping and Molecular Breeding of Tomato

    PubMed Central

    Foolad, Majid R.

    2007-01-01

    The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum × L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes ∼214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs. PMID:18364989

  6. Treatment of estrogens and androgens in dairy wastewater by a constructed wetland system.

    PubMed

    Cai, Kai; Elliott, Christopher T; Phillips, Debra H; Scippo, Marie-Louise; Muller, Marc; Connolly, Lisa

    2012-05-01

    Constructed wetland systems (CWS) have been used as a low cost bio-filtration system to treat farm wastewater. While studies have shown that CWS are efficient in removing organic compounds and pathogens, there is limited data on the presence of hormones in this type of treatment system. The objective of this study was to evaluate the ability of the CWS to reduce estrogenic and androgenic hormone concentration in dairy wastewater. This was achieved through a year long study on dairy wastewater samples obtained from a surface flow CWS. Analysis of hormonal levels was performed using a solid phase extraction (SPE) sample clean-up method, combined with reporter gene assays (RGAs) which incorporate relevant receptors capable of measuring total estrogenic or androgenic concentrations as low as 0.24 ng L(-1) and 6.9 ng L(-1) respectively. Monthly analysis showed a mean removal efficiency for estrogens of 95.2%, corresponding to an average residual concentration of 3.2 ng L(-1) 17β-estradiol equivalent (EEQ), below the proposed lowest observable effect concentration (LOEC) of 10 ng L(-1). However, for one month a peak EEQ concentration of 115 ng L(-1) was only reduced to 18.8 ng L(-1). The mean androgenic activity peaked at 360 ng L(-1) and a removal efficiency of 92.1% left an average residual concentration of 32.3 ng L(-1) testosterone equivalent (TEQ). The results obtained demonstrate that this type of CWS is an efficient system for the treatment of hormones in dairy wastewater. However, additional design improvements may be required to further enhance removal efficiency of peak hormone concentrations.

  7. An expanded genetic linkage map of Prunus based on an interspecific cross between almond and peach.

    PubMed

    Bliss, F A; Arulsekar, S; Foolad, M R; Becerra, V; Gillen, A M; Warburton, M L; Dandekar, A M; Kocsisne, G M; Mydin, K K

    2002-06-01

    The genetic linkage map of Prunus constructed earlier and based on an interspecific F2 population resulting from a cross between almond (Prunus dulcis D.A. Webb) and peach (Prunus persica L. Batsch) was extended to include 8 isozyme loci, 102 peach mesocarp cDNAs, 11 plum genomic clones, 19 almond genomic clones, 7 resistance gene analogs (RGAs), 1 RGA-related sequence marker, 4 morphological trait loci, 3 genes with known function, 4 simple sequence repeat (SSR) loci, 1 RAPD, and 1 cleaved amplified polymorphic sequence (CAP) marker. This map contains 161 markers placed in eight linkage groups that correspond to the basic chromosome number of the genus (x = n = 8) with a map distance of 1144 centimorgans (cM) and an average marker density of 6.8 cM. Four more trait loci (Y, Pcp, D, and SK) and one isozyme locus (Mdh1) were assigned to linkage groups based on known associations with linked markers. The linkage group identification numbers correspond to those for maps published by the Arús group in Spain and the Dirlewanger group in France. Forty-five percent of the loci showed segregation distortion most likely owing to the interspecific nature of the cross and mating system differences between almond (obligate outcrosser) and peach (selfer). The Cat1 locus, known to be linked to the D locus controlling fruit acidity, was mapped to linkage group 5. A gene or genes controlling polycarpel fruit development was placed on linkage group 3, and control of senesced leaf color (in late fall season) (LFCLR) was mapped to linkage group 1 at a putative location similar to where the Y locus has also been placed. PMID:12033621

  8. Thin-walled SnO₂ nanotubes functionalized with Pt and Au catalysts via the protein templating route and their selective detection of acetone and hydrogen sulfide molecules.

    PubMed

    Jang, Ji-Soo; Kim, Sang-Joon; Choi, Seon-Jin; Kim, Nam-Hoon; Hakim, Meggie; Rothschild, Avner; Kim, Il-Doo

    2015-10-21

    Bio-inspired Pt (∼2 nm) and Au (∼2.7 nm) catalysts encapsulated by a protein shell, i.e., Pt-apoferritin (Pt@AF) and Au-apoferriten (Au@AF), were synthesized via the hollow protein nanocage (apoferritin) templating route and directly functionalized on the interior and exterior walls of electrospun SnO2 nanotubes (NTs) during controlled single-nozzle electrospinning followed by high temperature calcination with heating rate control. Fast crystallization of the exterior shell and outward diffusion of the interior Sn precursors and crystallites result in the continued growth of a tubular wall, which is related to rapid heating driven Ostwald-ripening behavior. Very importantly, the Pt and Au nanoparticles (NPs) were immobilized onto thin-walled SnO2 NTs with a diameter of ∼350 nm and a shell thickness of ∼40 nm without any aggregation of catalysts due to high dispersibility, which originated from repulsive electrostatic (Coulombic) forces acting on the surface charged protein shells, leading to an enhanced catalytic effect and outstanding gas sensing properties. Pt-loaded SnO2 NTs exhibited superior acetone response (R(air)/R(gas) = 92 at 5 ppm) compared to pure SnO2 NFs (R(air)/R(gas) = 4.8 at 5 ppm) and SnO2 NTs (Rair/Rgas = 11 at 5 ppm) while Au-loaded SnO2 NTs showed a high response when exposed to hydrogen sulfide (R(air)/R(gas) = 34 at 5 ppm), offering selective gas detection with minimal cross-sensitivity against other interfering gases such as NH3, CO, NO, C6H5CH3, and C5H12. Our results provide a new insight into facile, cost-effective, and highly dispersible catalyst loading on the interior and exterior walls of hollow metal oxide NTs via simple electrospinning as a potential breath analyzer. PMID:26395290

  9. Sensing technologies for semiconductor process applications

    NASA Astrophysics Data System (ADS)

    Iturralde, Armando

    1995-09-01

    As semiconductor manufacturing technology advances, there exists a need to review improvements in process monitoring and control. Some of these improvements may be possible by investigating and integrating advanced process sensors. Sensors typically provide information to equipment controllers for proper machine operation. Expanding this definition, a sensor could deliver quality information about the semiconductor product being manufactured. Sensors can provide effective manufacturing line operation, reduced cycle times, and improved product quality. Implementing advanced sensors can also reduce process variability, increase process stability, and provide many other benefits applicable to modern semiconductor production operation. In this paper, a review of the current literature on semiconductor process sensor technology is presented. Much of the literature discusses in-situ measurements for film thickness, particles, and/or other conditions which could affect the quality of the product. Instruments such as RGAs (Residual Gas Analyzers), in-situ film thickness monitors represent current and future advanced sensors. Prior to implementing sensors, it would be ideal to reduce the number of process measurements as much as possible to insure sensor effectiveness. It will be ideal to have working cost of ownership model in place to baseline operations and monitor improvements as sensors move into the production line. There are many new sensors available with highly improved performance, accuracy, and even built-in electronics. These sensors can replace or supplement existing equipment sensors to improve performance, reliability, and extend equipment life. With the increasing costs of maintaining capital equipment, successful implementation could mean substantial savings. These and many other implementation issues are also presented.

  10. Srv mediated dispersal of streptococcal biofilms through SpeB is observed in CovRS+ strains.

    PubMed

    Connolly, Kristie L; Braden, Amy K; Holder, Robert C; Reid, Sean D

    2011-01-01

    Group A Streptococcus (GAS) is a human specific pathogen capable of causing both mild infections and severe invasive disease. We and others have shown that GAS is able to form biofilms during infection. That is to say, they form a three-dimensional, surface attached structure consisting of bacteria and a multi-component extracellular matrix. The mechanisms involved in regulation and dispersal of these GAS structures are still unclear. Recently we have reported that in the absence of the transcriptional regulator Srv in the MGAS5005 background, the cysteine protease SpeB is constitutively produced, leading to increased tissue damage and decreased biofilm formation during a subcutaneous infection in a mouse model. This was interesting because MGAS5005 has a naturally occurring mutation that inactivates the sensor kinase domain of the two component regulatory system CovRS. Others have previously shown that strains lacking covS are associated with decreased SpeB production due to CovR repression of speB expression. Thus, our results suggest the inactivation of srv can bypass CovR repression and lead to constitutive SpeB production. We hypothesized that Srv control of SpeB production may be a mechanism to regulate biofilm dispersal and provide a mechanism by which mild infection can transition to severe disease through biofilm dispersal. The question remained however, is this mechanism conserved among GAS strains or restricted to the unique genetic makeup of MGAS5005. Here we show that Srv mediated control of SpeB and biofilm dispersal is conserved in the invasive clinical isolates RGAS053 (serotype M1) and MGAS315 (serotype M3), both of which have covS intact. This work provides additional evidence that Srv regulated control of SpeB may mediate biofilm formation and dispersal in diverse strain backgrounds. PMID:22163320

  11. An in vitro investigation of endocrine disrupting effects of the mycotoxin alternariol

    SciTech Connect

    Frizzell, Caroline; Ndossi, Doreen; Kalayou, Shewit; Eriksen, Gunnar S.; Verhaegen, Steven; Sørlie, Morten; Elliott, Christopher T.; Ropstad, Erik; Connolly, Lisa

    2013-08-15

    Alternariol (AOH) is a mycotoxin commonly produced by Alternaria alternata on a wide range of foods. Few studies to date have been performed to evaluate the effects of AOH on endocrine activity. The present study makes use of in vitro mammalian cellular based assays and gene expression to investigate the ability of AOH to act as an endocrine disruptor by various modes of action. Reporter gene assays (RGAs), incorporating natural steroid hormone receptors for oestrogens, androgens, progestagens and glucocorticoids were used to identify endocrine disruption at the level of nuclear receptor transcriptional activity, and the H295R steroidogenesis assay was used to assess endocrine disruption at the level of gene expression and steroid hormone production. AOH exhibited a weak oestrogenic response when tested in the oestrogen responsive RGA and binding of progesterone to the progestagen receptor was shown to be synergistically increased in the presence of AOH. H295R cells when exposed to 0.1–1000 ng/ml AOH, did not cause a significant change in testosterone and cortisol hormones but exposure to 1000 ng/ml (3.87 μM) AOH resulted in a significant increase in estradiol and progesterone production. In the gene expression study following exposure to 1000 ng/ml (3.87 μM) AOH, only one gene NR0B1 was down-regulated, whereas expression of mRNA for CYP1A1, MC2R, HSD3B2, CYP17, CYP21, CYP11B2 and CYP19 was up-regulated. Expression of the other genes investigated did not change significantly. In conclusion AOH is a weak oestrogenic mycotoxin that also has the ability to interfere with the steroidogenesis pathway. - Highlights: • Alternariol was investigated for endocrine disrupting activity. • Reporter gene assays and the H295R steroidogenesis assay have been used. • An oestrogenic effect of alternariol was observed. • This can lead to an increase in expression of the progesterone receptor. • Alternariol is capable of modulating hormone production and gene expression.

  12. A single-dish survey of the HCO+, HCN, and CN emission toward the T Tauri disk population in Taurus

    NASA Astrophysics Data System (ADS)

    Salter, D. M.; Hogerheijde, M. R.; van der Burg, R. F. J.; Kristensen, L. E.; Brinch, C.

    2011-12-01

    detail, we find that two very different temperature and density disk structures produce very similar lines for the same underlying abundances. Instead, it is the gas properties (particularly Tkin and Rgas) and the projected kinematics (determined by M⋆ sin i) that have the largest impact on line appearance; and these system parameters are not well-constrained by current dust models, but instead will be probed directly with ALMA. Conclusions: Unresolved observations of the dust continuum provide neither a unique nor a complete picture of protoplanetary disks. Instead, gas-line measurements and resolved observations of dust and gas alike are needed to arrive at a full picture.

  13. Two alternative recessive quantitative trait loci influence resistance to spring black stem and leaf spot in Medicago truncatula

    PubMed Central

    Kamphuis, Lars G; Lichtenzveig, Judith; Oliver, Richard P; Ellwood, Simon R

    2008-01-01

    is tightly linked to a cluster of Toll/Interleukin1 receptor-nucleotide binding site-leucine-rich repeat (TIR-NBS-LRR) genes and disease resistance protein-like genes, while no resistance gene analogues (RGAs) are apparent in the genomic sequence of the reference accession A17 at the rnpm2 locus. Conclusion The induction of defence responses and cell death in the susceptible interaction following infection by P. medicaginis suggested this pathogen is not negatively affected by these responses and may promote them. A QTL for resistance was revealed in each of two populations derived from crosses between a resistant accession and two different susceptible accessions. Both loci are recessive in nature, and the simplest explanation for the existence of two separate QTLs is the occurrence of host genotype-specific susceptibility loci that may interact with undetermined P. medicaginis virulence factors. PMID:18366746