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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. Characterization of Resistance Gene Analogues (RGAs) in Apple (Malus × domestica Borkh.) and Their Evolutionary History of the Rosaceae Family

    PubMed Central

    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. PMID:24505246

  3. 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...

  4. Cloning and expression of resistance gene analogs (RGAs) from wild banana resistant to banana Fusarium wilt.

    PubMed

    Chen, Ya-Ping; Chen, Yun-Feng; Zhao, Jie-Tang; Huang, Xia; Huang, Xue-Lin

    2007-12-01

    Wild banana species are essential natural gene pools for banana improvement. In this study, six RGAs about 500 bp were obtained from leaves of Musa acuminata, a wild banana shown to be resistant to banana Fusarium wilt race 4, by PCR amplification with degenerate primers designed according to the conserved NBS motif and serine/threonine kinase domain of plant resistance (R) genes. Among these RGAs, the deduced amino acids of WNB1 and WNB2 contain NB-ARC domain and WNB1 can be translated into polypeptide uninterrupted by stop codons. The deduced amino acids of other four RGAs (WST1, WST2, WST3 and WST4) all contain the serine/threonine kinase domain and WST3 encodes a polypeptide homologous to that of bacterial blight resistance gene Xa21 of rice. At different time after inoculation with Fusarium oxysporum f. sp. cubense (FOC) race 4, the transcript patterns of WNB1 and WST3 was enhanced, which implied that the expression of WNB1 and WST3 may be related to the resistance of banana to Fusarium wilt. PMID:18349511

  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. Resistance Gene Analogs in Rosaceae: Family-wide Classification Including Raspberry, Cherry, and Wild Apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic studies have shown that NBS-LRR Resistance Gene Analogs (RGAs)tend to occur in clusters and often map to major resistance genes or QTLs. The identification and use of specific RGAs as molecular markers among plant material displaying different resistance phenotypes has the potential to direc...

  7. Resistance Gene Analogs in Cherries (Prunus spp.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic studies have shown that NBS-LRR Resistance Gene Analogs (RGAs) tend to occur in clusters and often map to major resistances gene or QTL. The identification and use of specific RGAs as molecular markers among plant material displaying differential resistance phenotypes has the potential to di...

  8. 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...

  9. 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...

  10. Isolation and Linkage Mapping of NBS-LRR Resistance Gene Analogs in Red Raspberry (Rubus idaeus L.) and Classification Among 269 Rosaceae NGS-LRR Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. Seventy-five putative resistance gene analogs (RGAs) containing conserved domains were cloned and sequenced from the red raspberry (Rubus idaeus L.) cultivar ‘Latham’ using degenerate primers based on RGA...

  11. 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. PMID:22411538

  12. Computational Reclassification of Resistance Gene Analogs in Rosaceae Based on the NBS-LRR Domain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. One hundred and ninety-five Rosaceae putative resistance gene analog (RGA) sequences containing conserved NBS-LRR domains were downloaded from the public domain. An additional seventy-six RGAs were amplif...

  13. 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

  14. 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.

  15. 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

  16. Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining.

    PubMed

    Bouktila, Dhia; Habachi-Houimli, Yosra; Khalfallah, Yosra; Mezghani-Khemakhem, Maha; Makni, Mohamed; Makni, Hanem

    2014-08-01

    In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, 'Salambo 80.' Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance. PMID:24638930

  17. 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.

  18. 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

  19. 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

  20. [Siebold and Ishizaka Sotetsu's contribution to the reception of acupuncture in nineteenth century Europe: a comparative research based on the acupuncture manuscripts in the Siebold collection].

    PubMed

    Mathias, Vigouroux; Machi, Senjuro

    2011-09-01

    This article examines Siebold and his relations with the Tokugawa shogunate acupuncture doctor Ishizaka Sotetsu, based on both Western and Japanese primary sources. It is well known that Siebold's contribution to a better understanding of Oriental medicine in Europe was limited to his interest in Japanese acupuncture, particularly Ishizaka Sotetsu's acupuncture. However, past research on this subject has only relied either on documents written in Dutch by Siebold's disciples or on Ishizaka Sotetsu's writings on acupuncture, therefore making it impossible to match the Dutch translations with the original Japanese manuscripts. This article brings new insights in Siebold's study on Ishizaka's acupuncture, investigating from a comparative point of view documents held by Leiden University, Leiden National Museum of Ethnology, Ruhr-Universittät Bochum, Toyo Bunko Library and the Ishizaka family's collection. The second part of the article analyzes also how Siebold's interest in Ishizaka Sotetsu's acupuncture differs from Rhyne's and Kaempfer's interest in Japanese acupuncture PMID:22397110

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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. PMID:27346232

  6. An in vitro investigation on the cytotoxic and nuclear receptor transcriptional activity of the mycotoxins fumonisin B1 and beauvericin.

    PubMed

    Fernández-Blanco, Celia; Frizzell, Caroline; Shannon, Maeve; Ruiz, Maria-Jose; Connolly, Lisa

    2016-08-22

    Fumonisin B1 (FB1) and beauvericin (BEA) are secondary metabolites of filamentous fungi, which under appropriate temperature and humidity conditions may develop on various foods and feeds. To date few studies have been performed to evaluate the toxicological and endocrine disrupting effects of FB1 and BEA. The present study makes use of various in vitro bioassays including; oestrogen, androgen, progestagen and glucocorticoid reporter gene assays (RGAs) for the study of nuclear receptor transcriptional activity, the thiazolyl blue tetrazolium bromide (MTT) assay to monitor cytotoxicity and high content analysis (HCA) for the detection of pre-lethal toxicity in the RGA and Caco-2 human colon adenocarcinoma cells. At the receptor level, 0.001-10μM BEA or FB1 did not induce any agonist responses in the RGAs. However at non-cytotoxic concentrations, an antagonistic effect was exhibited by FB1 on the androgen nuclear receptor transcriptional activity at 10μM and BEA on the progestagen and glucocorticoid receptors at 1μM. MTT analysis showed no decrease in cell viability at any concentration of FB1, whereas BEA showed a significant decrease in viability at 10μM. HCA analysis confirmed that the reduction in the progestagen receptor transcriptional activity at 1μM BEA was not due to pre-lethal toxicity. In addition, BEA (10μM) induced significant toxicity in both the TM-Luc (progestagen responsive) and Caco-2 cells. PMID:27234500

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. Highly Sensitive H2S Sensor Based on the Metal-Catalyzed SnO2 Nanocolumns Fabricated by Glancing Angle Deposition

    PubMed Central

    Yoo, Kwang Soo; Han, Soo Deok; Moon, Hi Gyu; Yoon, Seok-Jin; Kang, Chong-Yun

    2015-01-01

    As highly sensitive H2S gas sensors, Au- and Ag-catalyzed SnO2 thin films with morphology-controlled nanostructures were fabricated by using e-beam evaporation in combination with the glancing angle deposition (GAD) technique. After annealing at 500 °C for 40 h, the sensors showed a polycrystalline phase with a porous, tilted columnar nanostructure. The gas sensitivities (S = Rgas/Rair) of Au and Ag-catalyzed SnO2 sensors fabricated by the GAD process were 0.009 and 0.015, respectively, under 5 ppm H2S at 300 °C, and the 90% response time was approximately 5 s. These sensors showed excellent sensitivities compared with the SnO2 thin film sensors that were deposited normally (glancing angle = 0°, S = 0.48). PMID:26134105

  12. 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. PMID:26141566

  13. Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster.

    PubMed

    Kang, Houxiang; Weng, Yiqun; Yang, Yuhong; Zhang, Zhonghua; Zhang, Shengping; Mao, Zhenchuan; Cheng, Guohua; Gu, Xingfang; Huang, Sanwen; Xie, Bingyan

    2011-03-01

    Scab, caused by Cladosporium cucumerinum, is an important disease of cucumber, Cucumis sativus. In this study, we conducted fine genetic mapping of the single dominant scab resistance gene, Ccu, with 148 F(9) recombinant inbred lines (RILs) and 1,944 F(2) plants derived from the resistant cucumber inbred line 9110Gt and the susceptible line 9930, whose draft genome sequence is now available. A framework linkage map was first constructed with simple sequence repeat markers placing Ccu into the terminal 670 kb region of cucumber Chromosome 2. The 9110Gt genome was sequenced at 5× genome coverage with the Solexa next-generation sequencing technology. Sequence analysis of the assembled 9110Gt contigs and the Ccu region of the 9930 genome identified three insertion/deletion (Indel) markers, Indel01, Indel02, and Indel03 that were closely linked with the Ccu locus. On the high-resolution map developed with the F(2) population, the two closest flanking markers, Indel01 and Indel02, were 0.14 and 0.15 cM away from the target gene Ccu, respectively, and the physical distance between the two markers was approximately 140 kb. Detailed annotation of the 180 kb region harboring the Ccu locus identified a cluster of six resistance gene analogs (RGAs) that belong to the nucleotide binding site (NBS) type R genes. Four RGAs were in the region delimited by markers Indel01 and Indel02, and thus were possible candidates of Ccu. Comparative DNA analysis of this cucumber Ccu gene region with a melon (C. melo) bacterial artificial chromosome (BAC) clone revealed a high degree of micro-synteny and conservation of the RGA tandem repeats in this region. PMID:21104067

  14. Evaluation and modification of ASPEN fixed-bed gasifier models for inclusion in an integrated gasification combined-cycle power plant simulation

    SciTech Connect

    Stefano, J.M.

    1985-05-01

    Several Advanced System for Process Engineering (ASPEN) fixed-bed gasifier models have been evaluated to determine which is the most suitable model for use in an integrated gasification combined-cycle (IGCC) power plant simulation. Four existing ASPEN models were considered: RGAS, a dry ash gasifier model developed by Halcon/Scientific Design Company; USRWEN, the WEN II dry ash gasifier model originally developed by C.Y. Wen at West Virginia University; the slagging gasifier model developed by Massachusetts Institute of Technology (MIT) and based on Continental Oil Company's (CONOCO) design study for the proposed Pipeline Demonstration Plant; and the ORNL dry ash gasifier model developed by Oak Ridge National Laboratory for the simulation of the Tri-States Indirect Liquefaction Process. Because none of the models studied were suitable in their present form for inclusion in an IGCC power plant simulation, the SLAGGER model was developed by making significant modifications to the MIT model. The major problems with the existing ASPEN models were most often inaccurate material and energy balances, limitations of coal type, or long run times. The SLAGGER model includes simplifications and improvements over the MIT model, runs quickly (less than 30 seconds of computer time on a VAX-11/780), and gives more accurate mass and energy balances.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro).

    PubMed

    Gao, Z M; Li, C L; Peng, Z H

    2011-11-01

    Ma bamboo (Dendrocalamus latiflorus Munro) belongs to Dendrocalamus genus, Bambusease tribe, Bambusoideae subfamily, Poaceae family. It is a representative species of clumping bamboo, and a principal commercial species for various construction purposes using mature culms and for human consumption using young shoots. A normalized cDNA library was constructed from young leaves of Ma bamboo and 9,574 high-quality ESTs were generated, from which 5,317 unigenes including 1,502 contigs and 3,815 singletons were assembled. The unigenes were assigned into different gene ontology (GO) categories and summarized into 13 broad biologically functional groups according to similar functional characteristics or cellular roles by BLAST search against public databases. Eight hundred and ninety-one unigenes were assigned by KO identifiers and mapped to six KEGG biochemical pathways. The transcripts involved in biosynthesis of secondary metabolites such as cytochrome 450, flavonol synthase/flavanone 3-hydroxylase, and dihydroflavonol-4-reductase were well represented by 14 unigenes in the unigene set. The candidate genes involved in phytohormone metabolism, signal transduction and encoding cell wall-associated receptor kinases were also identified. Sixty-seven unigenes related to plant resistance (R) genes, including RPP genes, RGAs and RDL/RF genes, were discovered. These results will provide genome-wide knowledge about the molecular physiology of Ma bamboo young leaves and tools for advanced studies of molecular mechanism underlying leaf growth and development. PMID:21713530

  20. R gene expression changes related to Cercospora hydrangeae L.

    PubMed

    Kafantaris, Ioannis; Woodrow, Pasqualina; Carillo, Petronia

    2013-07-01

    Nursery growing as well as common landscape hydrangeas are all susceptible to leaf spot fungus Cercospora hydrangeae. Warm and rainy weather causes the fungal spores to germinate quickly and spread over the plant leaves forming small purple or brown spots. Although Hydrangea plants are not killed by leaf spot, it detracts from the value of plants through the reduction of flowering and plant vigor. The aim of our study was to isolate, characterize and investigate the expression profile of Hydrangea macrophylla resistance (R) gene transcripts under C. hydrangeae fungus infection and examine their evolutionary relationships by phylogenetic analysis. R-genes are thought to be one of the components of the genetic resistance in plants and most of them encode nucleotide binding site-leucine rich repeat (NBS-LRR) proteins. A cDNA-NBS strategy was carried out using as template cDNAs isolated from control and infected plant leaves. The cDNA-NBS profiling gave an excellent bands reproducibility. Twenty new transcripts corresponding to NBS-LRR proteins were identified only in infected plants. The extent of positivity between the aminoacid sequences at NBS region varied from 45 to 90 %, which indicates the diversity among the RGAs. The results of this paper will provide a genomic framework for the further isolation of candidate disease resistance NBS-encoding genes in Hortensia, and contribute to the understanding of the evolutionary mode of NBS-encoding genes in Hydrangeaceae crops. PMID:23644981

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

    PubMed

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

    2016-04-28

    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. PMID:26691720

  2. 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).

  3. 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

  4. A connection between extremely strong damped Lyman-α systems and Lyman-α emitting galaxies at small impact parameters

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    properties of the Ly α line (luminosity distribution, 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(Ly α) ≥ 1041erg s-1 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 = 2.5 kpc, i.e., significantly smaller than the radius corresponding to the BOSS fibre aperture, making fibre losses likely negligible. Finally, the average measured Ly α luminosity indicates a star-formation rate consistent with the Schmidt-Kennicutt law, SFR (M⊙ yr-1) ≈ 0.6 /fesc, where fesc < 1 is the Ly α escape fraction. Assuming the typical escape fraction of LAEs, fesc ~ 0.3, the Schmidt-Kennicutt law implies a galaxy radius of about rgal ≈ 2.5 kpc. Finally, we note that possible overestimation of the Ly α emission would result in both smaller rgas and rgal. Our results support a close association between LAEs and strong DLA host galaxies. Table 2 and Fig. 21 are available in electronic form at http://www.aanda.org

  5. 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

  6. 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. PMID:23485150

  7. 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

  8. Srv Mediated Dispersal of Streptococcal Biofilms Through SpeB Is Observed in CovRS+ Strains

    PubMed Central

    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

  9. Rpv10: a new locus from the Asian Vitis gene pool for pyramiding downy mildew resistance loci in grapevine.

    PubMed

    Schwander, Florian; Eibach, Rudolf; Fechter, Iris; Hausmann, Ludger; Zyprian, Eva; Töpfer, Reinhard

    2012-01-01

    A population derived from a cross between grapevine breeding strain Gf.Ga-52-42 and cultivar 'Solaris' consisting of 265 F1-individuals was genetically mapped using SSR markers and screened for downy mildew resistance. Quantitative trait locus (QTL) analysis revealed two strong QTLs on linkage groups (LGs) 18 and 09. The locus on LG 18 was found to be identical with the previously described locus Rpv3 and is transmitted by Gf.Ga-52-42. 'Solaris' transmitted the resistance-related locus on LG 09 explaining up to 50% of the phenotypic variation in the population. This downy mildew resistance locus is named Rpv10 for resistance to Plasmopara viticola. Rpv10 was initially introgressed from Vitis amurensis, a wild species of the Asian Vitis gene pool. The one-LOD supported confidence interval of the QTL spans a section of 2.1 centi Morgan (cM) corresponding to 314 kb in the reference genome PN40024 (12x). Eight resistance gene analogues (RGAs) of the NBS-LRR type and additional resistance-linked genes are located in this region of PN40024. The F1 sub-population which contains the Rpv3 as well as the Rpv10 locus showed a significantly higher degree of resistance, indicating additive effects by pyramiding of resistance loci. Possibilities for using the resistance locus Rpv10 in a grapevine breeding programme are discussed. Furthermore, the marker data revealed 'Severnyi' × 'Muscat Ottonel' as the true parentage for the male parent of 'Solaris'. PMID:21935694

  10. Mining, genetic mapping and expression analysis of EST-derived resistance gene homologs (RGHs) in cotton

    PubMed Central

    2014-01-01

    Background Cotton is the dominant textile crop and also serves as an important oil crop. An estimated 15% economic loss associated with cotton production in China has been caused by diseases, and no resistance genes have been cloned in this crop. Molecular markers developed from resistance gene homologues (RGHs) might be tightly linked with target genes and could be used for marker-assisted selection (MAS) or gene cloning. Results To genetically map expressed RGHs, 100 potential pathogenesis-related proteins (PRPs) and 215 resistance gene analogs (RGAs) were identified in the cotton expressed sequence tag database, and 347 specific primers were developed. Meanwhile, 61 cotton genome-derived RGA markers and 24 resistance gene analog polymorphism (RGAP) markers from published papers were included to view their genomic distribution. As a result, 38 EST-derived and 17 genome-derived RGH markers were added to our interspecific genetic map. These 55 markers were distributed on 18 of the 26 cotton chromosomes, with 34 markers on 6 chromosomes (Chr03, Chr04, Chr11, Chr17, Chr19 and Chr26). Homologous RGHs tended to be clustered; RGH clusters appeared on 9 chromosomes, with larger clusters on Chr03, Chr04 and Chr19, which suggests that RGH clusters are widely distributed in the cotton genome. Expression analysis showed that 19 RGHs were significantly altered after inoculation with the V991 stain of Verticillium dahliae. Comparative mapping showed that four RGH markers were linked with mapped loci for Verticillium wilt resistance. Conclusions The genetic mapping of RGHs confirmed their clustering in cotton genome. Expression analysis and comparative mapping suggest that EST-derived RGHs participate in cotton resistance. RGH markers are seemed to be useful tools to detected resistance loci and identify candidate resistance genes in cotton. PMID:25064562

  11. 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

  12. 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.

  13. Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection

    PubMed Central

    2012-01-01

    Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development. Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR. Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to

  14. 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