Sample records for rgas pazemes densgtvju

  1. Disease Resistance Gene Analogs (RGAs in Plants

    Manoj Kumar Sekhwal


    Full Text Available 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.

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

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


    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.

    Michele Perazzolli

    Full Text Available 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 × domestica Borkh.) and their evolutionary history of the Rosaceae family.

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


    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.

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

    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...

  6. Cloning and characterization of gene-resistant analogs (RGAs) involved in rust (Puccinia psidii) resistance in Eucalyptus grandis

    Marcelo Luiz Laia; Acelino Couto Alfenas; Sergio Hermnio Brommonschenkel; Shinitiro Oda; Eduardo Jose de Melo; Inae Marie de Arau jo Silva; Janana Fernandes Goncalves; Ariadne Marques


    Disease-resistant genes play an important role in defending against a variety of pathogens and insect pests in plants. Most of the disease-resistant genes encode pro-teins with conserved leucine rich repeat and nucleotide binding site domains. In this study, we cloned and char-acterized gene-resistant analogs (RGAs) from Eucalyptus grandis using degenerate PCR, with primers specifically targeting these two domains. The amplified fragments were cloned into the pGEM-T vector and transformed into Escherichia coli. Among the 90 clones obtained, 13 were sequenced and compared with each other and with previ-ously identified gene-resistant diseases. A BLASTX search in GenBank revealed high similarities among the con-served domains of these cloned genes with RGA genes. Some clones, however, showed no significant similarity with DNA sequences in GenBank. Southern blotting ana-lysis identified several polymorphic RFLP loci between distinct genotypes. However, none of them co-segregated with the Puccinia psidii Winter resistance gene 1 (Ppr1) in a population study.

  7. 亚洲棉5号染色体RGAs克隆与分析%Cloning and Analysis of RGAs from 5th Chromosome in Gossypiumn arboreum

    彭仁海; 程华; 刘方; 王春英; 黎绍惠; 张香娣; 王玉红; 王坤波


    棉花是最主要的天然纤维作物,深入进行棉花基因组研究具有重要意义.采用酶解、前后低渗和轻压相结合的方法制备亚洲棉染色体中期膜载片,激光法分离亚洲棉第5号单染色体,建单染色体扩增池后克隆其抗病基因同源序列(RGAs),获得P7、P12、P19和P23等4个序列.序列比对和聚类分析表明,这4条序列均为NBS-LRR类RGAs,P7、P12、P19聚成一类,它们之间的同源性很高,P23聚成另一类,与黑松的RPS2和油菜的RGA30同源性较高.为该染色体分子标记开发、基因克隆乃至全序列测定奠定基础.%Cotton is one of the main natural fiber crops. it is important to accumulate basic data in cotton genome research. The high quality metaphase chromosome membrane preparations of G. arboreum were obtained integrated with method of pre-hypotonicity, enzymolysis, post- hypotonicity and squashed with cover slide. A 5th chromosome was microdissected. Amplified production was obtained after the sequential procedures of protein-removing, enzymolysis and linker adaptor PCR (LA-PCR). A verified system was constructed after integrated the method of Southern blotting, SSR primer amplification and fluorescence in situ hybridization (FISH). Four nucleotide sequence P7, P12, P19 and P23 were obtained. The blast results showed that they are NBS-LRR-type resistant gene analog (RGA). Clustering analysis indicated that the sequences of P7, P12, P19 were high homologous and in the same cluster, the P23 was in other cluster and homologous with RPS2 gene of B. nigra and RGA30 gene of B. napus.

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

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


    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

  9. Identification and Cloning of Resistance Gene Analogues (RGAs) Encoding NBS-LRR Proteins from Gossypium arboreum L.

    AZHAR Muhammad Tehseen; BASHIR Afiab; BRIDDON Rob W; MANSOOR Shahid


    @@ Plants have developed a complicated defense mechanism during evolution to resist the harmful pathogens they encountered.The mechanism involves the interaction of the plant resistance (R) gene product with the component from the pathogen.This interaction further activates the signal transdue tion pathway,thus leading to defense responses.These defense responses include a hypersensitive response that results in localized cell death,and other general responses such as strengthening of the cell wall,formation of phytoalexins,etc.

  10. Isolation and characterization of resistance and defense gene analogs in cotton (Gossypium barbadense L.)

    GAO; Yulong; GUO; Wangzhen; WANG; Lei


    Plant disease resistance gene (R gene) and defense response gene encode some conserved motifs. In the present work, a PCR strategy was used to clone resistance gene analogs (RGAs) and defense gene analogs (DGAs) from Sea-island cotton variety Hai7124 using oligonucleotide primers based on the nucleotide-binding site (NBS) and serine/threonine kinase (STK) in the R-gene and pathogenesis-related proteins of class 2 (PR2) of defense response gene. 79 NBS sequences, 21 STK sequences and 11 DGAs were cloned from disease-resistance cotton. Phylogenic analysis of 79 NBS-RGAs and NBS-RGAs nucleotide sequences of cotton already deposited in GenBank identified one new sub-cluster. The deduced amino acid sequences of NBS-RGAs and STK-RGAs were divided into two distinct groups respectively: Toll/Interleukin-1 receptor (TIR) group and non-TIR group, A group and B group. The expression of RGAs and DGAs having consecutive open reading frame (ORF) was also investigated and it was found that 6 NBS-RGAs and 1 STK-RGA were induced, and 1 DGA was up-regulated by infection of Verticillium dahliae strain VD8. 4 TIR-NBS-RGAs and 4 non-TIR- NBS-RGAs were arbitrarily used as probes for Southern-blotting. There existed 2-10 blotted bands. In addition, since three non-TIR-NBS-RGAs have the same hybridization pattern, we conjecture that these three RGAs form a cluster distribution in the genome.

  11. Genome-wide identification of R genes and exploitation of candidate RGA markers in rice

    WANG Xusheng; WU Weiren; JIN Gulei; ZHU Jun


    By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or analogs (RGAs) and verified that RGAs are not randomly distributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By comparing the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (

  12. Identification of expressed resistance gene analogs (RGA and development of RGA-SSR markers in tobacco

    Yuan Qinghua


    Full Text Available Tobacco is an important cash crop and an ideal experimental system for studies of plant-pathogen interactions. Identification of tobacco resistance (R genes and resistance gene analogs (RGAs is propitious to elucidate the underlying resistant mechanisms. In recent years, the public tobacco EST (expressed sequence tags data set, which provides a rich source for identifying expressed RGAs, has enlarged substantially. In this study, 149606 Uni-ESTs were assembled from 412325 tobacco ESTs available in GenBank, scanned with 112 published plant R-genes protein sequences, and 1113 Nicotiana (tobacco RGAs (NtRGAs were identified. The majority of them comprised the common R-genes domains, such as NBS-LRR, LRR-PK, LRR, PK and Mlo, while we were unable to identify 109 RGAs using published domains of R-genes. Upon sequence alignment, 1079 NtRGAs were allocated on 712 loci within the Nicotiana benthamiana genome. A total of 78 simple sequence repeats (SSRs were identified from 72 NtRGAs, and out of 64 newly designed primer pairs, 54 primer pairs generated clear bands upon PCR amplification using tobacco genomic DNA. Only nine primer pairs displayed polymorphism in 24 varieties of tobacco, with 2-4 alleles per locus (2.56 alleles on average, while 41 primer pairs were able to detect polymorphisms in six wild species of genus Nicotiana, with 2-4 alleles per locus (2.61 alleles on average.

  13. Identifying resistance gene analogs associated with resistances to different pathogens in common bean.

    López, Camilo E; Acosta, Iván F; Jara, Carlos; Pedraza, Fabio; Gaitán-Solís, Eliana; Gallego, Gerardo; Beebe, Steve; Tohme, Joe


    ABSTRACT A polymerase chain reaction approach using degenerate primers that targeted the conserved domains of cloned plant disease resistance genes (R genes) was used to isolate a set of 15 resistance gene analogs (RGAs) from common bean (Phaseolus vulgaris). Eight different classes of RGAs were obtained from nucleotide binding site (NBS)-based primers and seven from not previously described Toll/Interleukin-1 receptor-like (TIR)-based primers. Putative amino acid sequences of RGAs were significantly similar to R genes and contained additional conserved motifs. The NBS-type RGAs were classified in two subgroups according to the expected final residue in the kinase-2 motif. Eleven RGAs were mapped at 19 loci on eight linkage groups of the common bean genetic map constructed at Centro Internacional de Agricultura Tropical. Genetic linkage was shown for eight RGAs with partial resistance to anthracnose, angular leaf spot (ALS) and Bean golden yellow mosaic virus (BGYMV). RGA1 and RGA2 were associated with resistance loci to anthracnose and BGYMV and were part of two clusters of R genes previously described. A new major cluster was detected by RGA7 and explained up to 63.9% of resistance to ALS and has a putative contribution to anthracnose resistance. These results show the usefulness of RGAs as candidate genes to detect and eventually isolate numerous R genes in common bean.

  14. Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (Citrus grandis) as a model. II. Cloning of resistance gene analogs from single chromosomes.

    Huang, D; Wu, W; Lu, L


    Amplification of resistance gene analogs (RGAs) is both a useful method for acquiring DNA markers closely linked to disease resistance (R) genes and a potential approach for the rapid cloning of R genes in plants. However, the screening of target sequences from among the numerous amplified RGAs can be very laborious. The amplification of RGAs from specific chromosomes could greatly reduce the number of RGAs to be screened and, consequently, speed up the identification of target RGAs. We have developed two methods for amplifying RGAs from single chromosomes. Method 1 uses products of Sau3A linker adaptor-mediated PCR (LAM-PCR) from a single chromosome as the templates for RGA amplification, while Method 2 directly uses a single chromosomal DNA molecule as the template. Using a pair of degenerate primers designed on the basis of the conserved nucleotide-binding-site motifs in many R genes, RGAs were successfully amplified from single chromosomes of pomelo using both these methods. Sequencing and cluster analysis of RGA clones obtained from single chromosomes revealed the number, type and organization of R-gene clusters on the chromosomes. We suggest that Method 1 is suitable for analyzing chromosomes that are unidentifiable under a microscope, while Method 2 is more appropriate when chromosomes can be clearly identified.

  15. 使用在线RGA的先进半导体生产%Advanced Semiconductor Manufacturing with an in situ RGA



    Automated residual gas analyzers (RGAs) canplay a very important role in advanced process con-trol (APC), advanced equipment control (AEC), andfault detection and classification (FDC). Inparticular, automated RGAs can provide needed tooland process information to aid in such analyses.This paper will discuss the role that automated RGAcan play in the areas of APC, AEC, and FDC, presenta viable automated RGA approach, and lastly, pro-vide an example of this approach to the detectionof photoresist.

  16. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

    Irfan A Ghazi; Prem S Srivastava; Vivek Dalal; Kishor Gaikwad; Ashok K Singh; Tilak R Sharma; Nagendra K Singh; Trilochan Mohapatra


    Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

  17. Creating of Regional Hydrogeological Model for South-East of Lithuania

    Spalviņš, A; Šlangens, J; Lāce, I; Stuopis, A; Domasevicius, A


    Izveidots reģionālais hidroģeoloģiskais modelis (HM) Kvartāra tipa pazemes ūdeņu sistēma, kura atrodas Lietuvas Dienvidaustrumu daļā. Šī sistēma pārklāj Lietuvas teritorijas vienu trešdaļu. HM taisnstūra formas laukuma izmērs ir 290km210km. Seši lokālie upju sateces baseini veido HM aktīvo daļu, kurai ir neregulāra forma. Modeļa daļa, kura nav aktīva, nepiedalās aprēķinos. HM veidošanai izmantotas inovatīvas metodes: zemes virsmas augstumu karte kā pjezometrisko ūdens līmeņu robežnoteikumu, ...

  18. Cloning and Characterization of a Family of Disease Resistance Gene Analogs from 6VS of Haynaldia villosa

    KONG Fan-jing; MA You-zhi; CHEN Xiao; XIN Zhi-yong


    In the present study, microdissection of 6VS and the cloning of the resistance gene analogs (RGA) from them were reported. The 6VS were microdissected with needle and 10 types of resistance gene analogs were obtained by PCR with degenerate oligonucleotide primer designed according to resistance genes. They were designated as Hvrgak1-Hvrgak10, GenBank accession numbers are AF387113-AF387121,AY040671- AY040672. Identity among RGAs was about 10-50%, and identity with cloned R gene from plants was 5-20%. Southern hybridization analysis results showed 3 RGAs, Hvrgak2, Hvrgak4, and Hvrgak5 were linked with wheat powdery mildew resistance. These RGAs may be used as direct entrance or probes for cloning the disease resistance genes.

  19. Diversity and evolutionary relationship of nucleotide binding site-encoding disease-resistance gene analogues in sweet potato (Ipomoea batatas Lam.)

    Guanshui Chen; Daren Pan; Yifei Zhou; Sheng Lin; Xiangde Ke


    Most plant disease-resistance genes (-genes) isolated so far encode proteins with a nucleotide binding site (NBS) domain and belong to a superfamily. NBS domains related to -genes show a highly conserved backbone of an amino acid motif, which makes it possible to isolate resistance gene analogues (RGAs) by degenerate primers. Degenerate primers based on the conserved motif (P-loop and GLPL) of the NBS domain from -genes were used to isolate RGAs from the genomic DNA of sweet potato cultivar Qingnong no. 2. Five distinct clusters of RGAs (22 sequences) with the characteristic NBS representing a highly diverse sample were identified in sweet potato genomic DNA. Sequence identity among the 22 RGA nucleotide sequences ranged from 41.2% to 99.4%, while the deduced amino acid sequence identity from the 22 RGAs ranged from 20.6% to 100%. The analysis of sweet potato RGA sequences suggested mutation as the primary source of diversity. The phylogenetic analyses for RGA nucleotide sequences and deduced amino acids showed that RGAs from sweet potato were classified into two distinct groups—toll and interleukin receptor-1 (TIR)-NBS-LRR and non-TIR-NBS-LRR. The high degree of similarity between sweet potato RGAs and NBS sequences derived from -genes cloned from tomato, tobacco, flax and potato suggest an ancestral relationship. Further studies showed that the ratio of non-synonymous to synonymous substitution within families was low. These data obtained from sweet potato suggest that the evolution of NBS-encoding sequences in sweet potato occur by the gradual accumulation of mutations leading to purifying selection and slow rates of divergence within distinct -gene families.

  20. Investigation of the Hypersonic Flowfield Surrounding a Shaped Charge Jet.



  1. Identification and characterization of a resistance gene analog (RGA) from the Caricaceae Dumort family = Identificação e caracterização de um análogo de gene de resistência (AGR) da família de Caricaceae Dumort

    Amaral, P.P.R.; Alves, P.C.M.; Martins, N.F.; Silva, F.R.; Capdeville, G.; Souza, M.T.


    The majority of cloned resistance (R) genes characterized so far contain a nucleotide-binding site (NBS) and a leucine-rich repeat (LRR) domain, where highly conserved motifs are found. Resistance genes analogs (RGAs) are genetic markers obtained by a PCR-based strategy using degenerated oligonucleo

  2. 77 FR 18176 - Magnuson-Stevens Fishery Conservation and Management Act Provisions; Fisheries of the...


    ... International Fisheries Agreement Clarification Act (IFACA) enacted into law on January 4, 2011, the Council and... part of a trip in these RGAs to use a haddock separator trawl, a Ruhle trawl, a rope trawl, longline... gear type), the rope trawl, and any other gears authorized by the Council in a management action...

  3. Identification and characterization of a resistance gene analog (RGA) from the Caricaceae Dumort family = Identificação e caracterização de um análogo de gene de resistência (AGR) da família de Caricaceae Dumort

    Amaral, P.P.R.; Alves, P.C.M.; Martins, N.F.; Silva, F.R.; Capdeville, G.; Souza, M.T.


    The majority of cloned resistance (R) genes characterized so far contain a nucleotide-binding site (NBS) and a leucine-rich repeat (LRR) domain, where highly conserved motifs are found. Resistance genes analogs (RGAs) are genetic markers obtained by a PCR-based strategy using degenerated oligonucleo

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

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


    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.

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

    Wan Hongjian


    Full Text Available Abstract 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

  6. Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping

    Souza Manoel T


    Full Text Available Abstract Background Many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. Fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (R-genes. The largest known family of plant R-genes encode proteins with nucleotide-binding site (NBS and C-terminal leucine-rich repeat (LRR domains. Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence. Results A computational strategy was developed for unbiased conserved motif discovery in NBS and LRR domains in R-genes and homologues in monocotyledonous plant species. Degenerate PCR primers targeting conserved motifs were tested on the wild cultivar Musa acuminata subsp. burmannicoides, var. Calcutta 4, which is resistant to a number of fungal pathogens and nematodes. One hundred and seventy four resistance gene analogs (RGAs were amplified and assembled into 52 contiguous sequences. Motifs present were typical of the non-TIR NBS-LRR RGA subfamily. A phylogenetic analysis of deduced amino-acid sequences for 33 RGAs with contiguous open reading frames (ORFs, together with RGAs from Arabidopsis thaliana and Oryza sativa, grouped most Musa RGAs within monocotyledon-specific clades. RFLP-RGA markers were developed, with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid M. acuminata mapping population. Eighty eight BAC clones were identified in M. acuminata Calcutta 4, M. acuminata Grande Naine, and M. balbisiana Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes. Multiple copy RGAs were common within BAC clones, potentially representing variation reservoirs for evolution of new R-gene specificities. Conclusion This is the first large scale analysis of NBS-LRR RGAs in M. acuminata Calcutta 4. Contig sequences were

  7. Identificación de genes análogos de resistencia a enfermedades en yuca (Manihot esculenta Crantz y su relación con la resistencia a tres especies de Phytophthora

    Fregene M


    Full Text Available Los genes de resistencia se buscaron mediante dos estrategias. La primera, por medio de hibridización con sondas de maíz y arroz, utilizando RFLP. La segunda consistió en la amplificación de regiones conservadas de ADN, con cebadores degenerados NBS y Pto kinasa, en tres genotipos de yuca resistentes a Phytophthora tropicalis y P. palmivora, obteniendo clones que se secuenciaron y se homologaron con genes de resistencia conocidos. Con las secuencias se diseñaron cebadores específicos que permitieron amplificar regiones de ADN de los parentales e individuos resistentes y susceptibles. Las bandas se separaron mediante electroforesis en geles de poliacrilamida denaturantes y no denaturantes (SSCP - polimorfismo en la conformación de cadenas simples. Se identificaron cinco QTLs asociados con resistencia a Phytophthora. La yuca tuvo muy baja homología con los genes de maíz y arroz. Se obtuvieron 28 clones NBS y 2 Pto kinasa, de los cuales 5 mostraron secuencia homóloga con RGAs (genes análogos de resistencia NBS-LRR y cuatro de ellos mostraron marco abierto de lectura con motivos conservados de la región NBS, y se consideraron como RGAs. Se identificaron tres clases de RGAs aunque no hubo evidencia de su asociación con resistencia a Phytophthora. Palabras claves: Yuca, Phytophthora, QTLs, RGAs, sondas, cebadores degenerados. ABSTRACT Identification of gene analogs for resistance to cassava (Manihot esculenta Crantz Diseases, and their relationship to resistance to three Phytophthora species. Two strategies were used to find resistance genes in cassava. The first through hybridizing probes from maize and rice, using RFLP. The second strategy consisted of amplifying conserved regions of DNA, with degenerated NBS and Pto kinase primers, in three cassava genotypes resistant to Phytophthora tropicalis and P. palmivora, obtaining clones that were sequenced and compared with known resistance genes. Specific primers were designed from

  8. Identification of Expressed Resistance Gene Analogs from Peanut (Arachis hypogaea L.) Expressed Sequence Tags

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


    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 AhlV.These expressed RGAs are the source for RGA-tagged marker development and identification of peanut resistance genes.

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

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


    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.

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

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


    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.

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

    Yoon, Seokkwan; Jost, Gabriele; Chang, Sherry


    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.

  12. Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance.

    Geffroy, V; Sévignac, M; De Oliveira, J C; Fouilloux, G; Skroch, P; Thoquet, P; Gepts, P; Langin, T; Dron, M


    Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.

  13. First Wall and Operational Diagnostics

    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


    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.

  14. PÖFFi esimene seeria / Erkki Luuk

    Luuk, Erkki, 1971-


    Pimedate Ööde filmifestivalil näidatud filme - animafilm "Ärgas elu" ("Waking Life") : režissöör Richard Linklater : Ameerika Ühendriigid 2001, mängufilm "Kana süda" 8"Chicken Heart") : režissöör Hiroshi Shimizu : Jaapan 2002 ja Ida-Saksamaa indiaanifilm "Chingachguk - Suur Madu" ("Chinachgook - die Grosse Schlange") : režissöör Richard Groschopp : 1967, mis oli üks serblasest filminäitleja Gojko Mitic'i retrospektiivi kuulunud filmidest

  15. PÖFFi esimene seeria / Erkki Luuk

    Luuk, Erkki, 1971-


    Pimedate Ööde filmifestivalil näidatud filme - animafilm "Ärgas elu" ("Waking Life") : režissöör Richard Linklater : Ameerika Ühendriigid 2001, mängufilm "Kana süda" 8"Chicken Heart") : režissöör Hiroshi Shimizu : Jaapan 2002 ja Ida-Saksamaa indiaanifilm "Chingachguk - Suur Madu" ("Chinachgook - die Grosse Schlange") : režissöör Richard Groschopp : 1967, mis oli üks serblasest filminäitleja Gojko Mitic'i retrospektiivi kuulunud filmidest

  16. 40 CFR 63.365 - Test methods and procedures.


    ...=standard volume, 24.05 liters per mole (L/mole)=22.414 L/mole ideal gas law constant corrected to 20 °C and 101.325 kPa (385.32 scf per mole (scf/mole)=359 scf/mole ideal gas law constant corrected to 68 °F and...Pa (psia) V=chamber volume, liters (L) (ft3) R=gas constant, 8.313 L·kPa/g-mole·(10.73...

  17. Multiphase Heat and Mass Transfer Through Hygroscopic Porous Media with Applications to Clothing Materials


    epsrhov,iwrite,nprint,aL,aL2,ddry,dwet,dhvap, lql,header,tkss,cpss,rhoss, edss ,edsa,edsh,amu,amus,xmn2, lykdarc,xkdarc,deltap,pinch,facttop,factbot...flow in sample section of cell DO 103 I=isbeg,isend DO 103 J=JSBEG,JSEND t(i,j)=tint xmdot(i,j)=0.D0 EDS(i,j)= edss C*****INITIAL SAMPLE WATER...TKA, 1CPDS,CPW,CPV,CPA,PATM,RGAS,XMW,XMA,CHTC,CMTC,dsolid, lmethod,epsrhov,iwrite,nprint,aL,aL2,ddry,dwet,dhvap, lql,header,tkss,cpss,rhoss, edss

  18. Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny

    Abbott Albert


    Full Text Available Abstract Background Fragaria belongs to the Rosaceae, an economically important family that includes a number of important fruit producing genera such as Malus and Prunus. Using genomic sequences from 50 Fragaria fosmids, we have examined the microsynteny between Fragaria and other plant models. Results In more than half of the strawberry fosmids, we found syntenic regions that are conserved in Populus, Vitis, Medicago and/or Arabidopsis with Populus containing the greatest number of syntenic regions with Fragaria. The longest syntenic region was between LG VIII of the poplar genome and the strawberry fosmid 72E18, where seven out of twelve predicted genes were collinear. We also observed an unexpectedly high level of conserved synteny between Fragaria (rosid I and Vitis (basal rosid. One of the strawberry fosmids, 34E24, contained a cluster of R gene analogs (RGAs with NBS and LRR domains. We detected clusters of RGAs with high sequence similarity to those in 34E24 in all the genomes compared. In the phylogenetic tree we have generated, all the NBS-LRR genes grouped together with Arabidopsis CNL-A type NBS-LRR genes. The Fragaria RGA grouped together with those of Vitis and Populus in the phylogenetic tree. Conclusions Our analysis shows considerable microsynteny between Fragaria and other plant genomes such as Populus, Medicago, Vitis, and Arabidopsis to a lesser degree. We also detected a cluster of NBS-LRR type genes that are conserved in all the genomes compared.

  19. Ag-doped titanium dioxide gas sensor

    Alaei Sheini, Navid; Rohani, Mahsa


    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.

  20. PRGPred: A platform for prediction of domains of resistance gene analogue (RGA in Arecaceae developed using machine learning algorithms



    Full Text Available Plant disease resistance genes (R-genes are responsible for initiation of defense mechanism against various phytopathogens. The majority of plant R-genes are members of very large multi-gene families, which encode structurally related proteins containing nucleotide binding site domains (NBS and C-terminal leucine rich repeats (LRR. Other classes possess' an extracellular LRR domain, a transmembrane domain and sometimes, an intracellular serine/threonine kinase domain. R-proteins work in pathogen perception and/or the activation of conserved defense signaling networks. In the present study, sequences representing resistance gene analogues (RGAs of coconut, arecanut, oil palm and date palm were collected from NCBI, sorted based on domains and assembled into a database. The sequences were analyzed in PRINTS database to find out the conserved domains and their motifs present in the RGAs. Based on these domains, we have also developed a tool to predict the domains of palm R-genes using various machine learning algorithms. The model files were selected based on the performance of the best classifier in training and testing. All these information is stored and made available in the online ‘PRGpred' database and prediction tool.

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

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


    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. Caracterização genética de espécies de Passiflora por marcadores moleculares análogos a genes de resistência Genetic characterization of Passiflora species via resistance genes analog markers

    Mariana da Silva Paula


    Full Text Available O cultivo comercial do maracujá é afetado por diversos problemas fitossanitários, os quais contribuem para quebras de produção e significativa redução da vida útil dos plantios. Em algumas situações, a incidência de doenças pode inviabilizar o cultivo do maracujá. Fontes de resistência a distintas doenças têm sido identificadas em acessos de espécies de Passiflora. Neste trabalho, buscou-se avaliar a diversidade genética de acessos de oito espécies silvestres (P. setacea, P. nitida, P. serratodigitata, P. caerulea, P. gibertii, P. odontophyla, P. edulis e P. coccinea e de um híbrido interespecífico (P. setacea x P. coccinea, utilizando marcadores moleculares análogos a genes de resistência (RGAs. Verificou-se uma grande diversidade no perfil eletroforético de RGAs nos acessos de Passiflora, permitindo a anotação de 96 amplicons polimórficos entre, pelo menos, um par de acessos. Os níveis de dissimilaridade genética (calculados exclusivamente com os marcadores RGAs variaram entre 0,40 e 0,89 nos acessos das espécies de Passiflora avaliadas. A análise de sequência de um subgrupo destes amplicons obtidos com primers RGAs indicou que estas bandas correspondem a regiões genômicas que contêm segmentos (motivos com identidade aos encontrados em genes de resistência previamente caracterizados em outras espécies vegetais. Desta forma, os dados indicam a existência de um repertório variado de marcadores do tipo RGA em Passiflora que podem ser potencialmente úteis em sistemas de caracterização molecular de germoplasma e em programas de melhoramento genético visando à resistência a doenças nesta cultura.The commercial cultivation of passion fruit can be affected by many diseases, which might induce sever fruit yield losses and significant life cycle reduction of the crop. In some situations disease incidence can make the passion fruit production not economically viable. Sources of resistance against several

  3. 绿豆NBS-LRR类抗病基因同源序列的克隆与分析%Cloning and Analysis of NBS-LRR Type Resistance Gene Analogues in Vigna radiata

    罗灵杰; 周以飞; 柯兰兰; 潘大仁


    根据已知的拟南芥 S PR2基因、烟草抗花叶病毒 N 基因、亚麻 L6基因等 NBS-LRR抗病类基因(RGAs)保守序列设计引物,从野生绿豆基因组DNA 中分离得到了1条515 bp大小的目的片段,并命名为FGV-1(GenBank登录号为KF021265)。经BLAST分析表明,分离的绿豆RGAs与已报道的大豆、豇豆、芸豆等植物的RGAs有较高的同源性。通过对其编码的氨基酸序列分析表明, FGV-1基因翻译的氨基酸序列中含有植物抗病基因NBS-LRR区域的4个保守结构:GMGGVGKTT 、LILDDVD、GSRVIVTTRD及GLPLA ,推测FGV-1可能是绿豆NBS-LRR类抗性基因的核心区域。绿豆RGAs的分离将为进一步从绿豆中分离功能性抗病基因打下基础,也为研究绿豆种质资源的起源与进化提供借鉴。%Degenerate primers based on conserved sequences of the nucleotide binding site and 1eucine rich repeats (NBS-LRR) region from the cloned plant disease resistance genes were used to isolate resistance gene analogues (RGAs) from genomic DNA of Vigna radiata .The desired band (515bp) was cloned and sequenced .The band was named FGV-1 and had been submitted to Genbank (accession number KF021265) .Blastx analys showed highly homology with the reported resistance gene analogues Glycine max ,Vigna unguiculata and Phaseolus vulgaris . The analysis of RGAs amino acid sequence structures suggested that FGV-1 was the core region of NBS-LRR resistance genes in Vigna radiata ,which contained four conserved domains including GMGGVGKTT ,LILDDVD , GSRVIVTTRD and GLPLAL .The RGAs isolated from Vigna radiata used in this study would provide the base for the further cloning of disease-resistance genes in V igna radiata ,and provide reference for the origin and evolution of V igna radiata .

  4. Real-Code Genetic Algorithm for Ground State Energies of Hydrogenic Donors in GaAs-(Ga,Al)As Quantum Dots

    YAN Hai-Qing; TANG Chen; LIU Ming; ZHANG Hao


    We present a global optimization method, called the real-code genetic algorithm (RGA), to the ground state energies. The proposed method does not require partial derivatives with respect to each variational parameter or solving an eigenequation, so the present method overcomes the major difficulties of the variational method. RGAs also do not require coding and encoding procedures, so the computation time and complexity are reduced. The ground state energies of hydrogenic donors in GaAs-(Ga,Al)As quantum dots have been calculated for a range of the radius of the quantum dot radii of practical interest. They are compared with those obtained by the variational method. The results obtained demonstrate the proposed method is simple, accurate, and easy implement.

  5. Identification of QTLs for early blight ( Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross.

    Foolad, R.; Zhang, P.; Khan, A. A.; Niño-Liu, D.; Lin, Y.


    Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal ( Alternaria solani Sorauer) disease of tomato in the northern and eastern parts of the U.S. and elsewhere in the world. The disease causes plant defoliation, which reduces yield and fruit quality, and contributes to significant crop loss. Sources of resistance have been identified within related wild species of tomato. The purpose of this study was to identify and validate quantitative trait loci (QTLs) for EB resistance in backcross populations of a cross between a susceptible tomato breeding line (NC84173; maternal and recurrent parent) and a resistant Lycopersicon hirsutum Humb. and Bonpl. accession (PI126445). Sixteen hundred BC(1) plants were grown to maturity in a field in 1998. Plants that were self-incompatible, indeterminant in growth habit, and/or extremely late in maturity, were discarded in order to eliminate confounding effects of these factors on disease evaluation, QTL mapping, and future breeding research. The remaining 145 plants (referred to as the BC(1) population) were genotyped for 141 restriction fragment length polymorphism (RFLP) markers and 23 resistance gene analogs (RGAs), and a genetic linkage map was constructed. BC(1) plants were evaluated for disease symptoms throughout the season, and the area under the disease progress curve (AUDPC) and the final percent defoliation (disease severity) were determined for each plant. BC(1) plants were self-pollinated and produced BC(1)S(1) seed. The BC(1)S(1) population, consisting of 145 BC(1)S(1) families, was grown and evaluated for disease symptoms in replicated field trials in two subsequent years (1999 and 2000) and AUDPC and/or final percent defoliation were determined for each family in each year. Two QTL mapping approaches, simple interval mapping (SIM) and composite interval mapping (CIM), were used to identify QTLs for EB resistance in the BC(1) and BC(1)S(1

  6. Cloning and Analysis of NBS-LRR Disease-Resistant Gene Analogs in Citrus unshiu Marc.%晚熟温州蜜柑 NBS-LRR类抗病基因同源序列的克隆及分析

    刘登全; 王园秀; 崔朝宇; 秦双林; 欧阳慧; 蒋军喜


    为加深对柑橘黄龙病抗性机理的了解和为黄龙病抗性基因的克隆提供依据,根据已知植物抗病基因NBS-LRR保守结构域设计简并引物,以柑橘黄龙病抗性品种“晚熟温州蜜柑”为供试材料,对其基因组DNA进行PCR扩增、克隆和序列测定,结果共获得17条抗病基因同源序列(resistance gene analogs,RGAs),其在NCBI中的登录号为KJ019189~KJ019199,KR815564~KR815569。序列分析表明,这17个RGAs与甜橙、柚等柑橘属中推测的一些抗病蛋白基因或其他相关蛋白基因具有显著高的同源性。其中一些RGAs与拟南芥抗霜霉病RPP13基因、柑橘抗衰退病毒基因Ctv或烟草抗TMV基因N具有51.7%~79.0%的氨基酸序列同源性。依据论文结果,笔者认为,晚熟温州蜜柑中存在较丰富的NBS-LRR类抗病基因,但具体哪些病基因与抗黄龙病相关尚需进一步研究。%In order to deepen understanding of the resistant mechanism of Citrus to Candiadatus Liberi-bacter asiaticus( CLas) and lay the foundation for cloning of citrus huanglongbing( HLB)-resistant gene,a pair of degenerate primers was designed from the conserved domains of NBS-LRR type plant disease-resistant gene and used for amplifying the disease-resistant gene analogs( RGAs) by polymerase chain reaction( PCR) from the genomic DNA of Citrus unshiu Marc.,a citrus cultivar resistant to HLB.After cloning and sequencing the PCR products,the nucleotide sequences and their deduced amino acid sequences of 17 RGAs were obtained and deposited in GenBank with the accession number of KJ019189-KJ019199 and KR815564-KR815569.Se-quence analysis showed that these 17 RGAs shared significantly high homology with some putative disease-re-sistant genes and other protein genes in Citrus sinensis or Citrus clementina, some of which shared 51.7%-79.0%amino acid sequence homology with the known disease gene of RPP13,Ctv,or N.Based on these re-sults,it is concluded

  7. De novo foliar transcriptome of Chenopodium amaranticolor and analysis of its gene expression during virus-induced hypersensitive response.

    Yongqiang Zhang

    Full Text Available BACKGROUND: The hypersensitive response (HR system of Chenopodium spp. confers broad-spectrum virus resistance. However, little knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence, we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, a Chenopodium species widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. METHODOLOGY AND PRINCIPAL FINDINGS: Using Illumina HiSeq™ 2000 platform, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,452 unigenes (3,847 clusters and 108,605 singletons. BlastX search against the NCBI NR database identified 61,698 sequences with a cut-off E-value above 10(-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms, respectively. A total number of 738 resistance gene analogs (RGAs and homology sequences of 6 key signaling proteins within the R proteins-directed signaling pathway were identified. Based on this transcriptome data, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus by using digital gene expression analysis. Numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR were identified, and the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were particularly emphasized. CONCLUSIONS: To our knowledge, this study is the first description of the genetic makeup of C. amaranticolor, providing deep insight into the comprehensive gene expression information at transcriptional level in this species. The 738 RGAs as well as the differentially regulated genes, particularly the common genes regulated by both TMV and CMV, are suitable candidates which merit further

  8. LINKAGE MAPPING OF CANDIDATE GENES FOR INDUCE RESISTANCE AND GROWTH PROMOTION BY Trichoderma koningiopsis (Th003 IN TOMATO Solanum lycopersicum Mapeo de genes candidatos relacionados con inducción de resistencia sistemica y promoción de crecimiento por Trichoderma koningiopsis (Th003 en tomate Solanum lycopersicum



    Full Text Available Induced systemic resistance (ISR is a mechanism by which plants enhance defenses against any stress condition. ISR and growth promotion are enhanced when tomato (Solanum lycopersicum is inoculated with several strains of Trichoderma ssp. This study aims to genetically map tomato candidate genes involved in ISR and growth promotion induced by the Colombian native isolate Trichoderma koningiopsis Th003. Forty-nine candidate genes previously identified on tomato plants treated with Th003 and T. hamatum T382 strains were evaluated for polymorphisms and 16 of them were integrated on the highly saturated genetic linkage map named “TOMATO EXPEN 2000”. The location of six unigenes was similar to the location of resistance gene analogs (RGAs, defense related ESTs and resistance QTLs previously reported, suggesting new possible candidates for these quantitative trait loci (QTL regions. The candidate gene-markers may be used for future ISR or growth promotion assisted selection in tomato.La resistencia sistémica inducida (ISR es un mecanismo mediante el cual las plantas aumentan sus defensas frente a cualquier condición de estrés. El objetivo de este trabajo fue localizar en el mapa genético de tomate, genes candidatos involucrados en ISR y promoción de crecimiento inducidos por la cepa colombiana nativa Th003 de Trichoderma koningiopsis. Se realizó una búsqueda de polimorfismos en cuarenta y nueve genes candidatos previamente identificados en plantas de tomate inoculadas con Th003 y la cepa T382 de T. hamatum. Diez y seis de estos genes candidatos fueron integrados en el mapa genético de tomate altamente saturado, llamado “TOMATO EXPEN 2000”. La ubicación de seis unigenes fue similar a la localización de genes análogos de resistencia (RGAs, ESTs relacionados con defensa y QTLs de resistencia previamente identificados, sugiriendo posibles nuevos candidatos para estas regiones de QTLs. Los genes candidatos o marcadores pueden ser usados

  9. A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross.

    Zhang, L P; Khan, A; Niño-Liu, D; Foolad, M R


    A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with

  10. Organization, expression and evolution of a disease resistance gene cluster in soybean.

    Graham, Michelle A; Marek, Laura Fredrick; Shoemaker, Randy C


    PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar "Williams 82" [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca(2+)-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process. PMID:12524363

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

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


    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.

  12. Identification and characterization of a NBS–LRR class resistance gene analog in Pistacia atlantica subsp. Kurdica

    Bahman Bahramnejad


    Full Text Available P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plant which grows in Kurdistan, Iran. The identification of resistance gene analogs holds great promise for the development of resistant cultivars. A PCR approach with degenerate primers designed according to conserved NBS-LRR (nucleotide binding site-leucine rich repeat regions of known disease-resistance (R genes was used to amplify and clone homologous sequences from P. atlantica subsp. Kurdica. A DNA fragment of the expected 500-bp size was amplified. The nucleotide sequence of this amplicon was obtained through sequencing and the predicted amino acid sequence compared to the amino acid sequences of known R-genes revealed significant sequence similarity. Alignment of the deduced amino acid sequence of P. atlantica subsp. Kurdica resistance gene analog (RGA showed strong identity, ranging from 68% to 77%, to the non-toll interleukin receptor (non-TIR R-gene subfamily from other plants. A P-loop motif (GMMGGEGKTT, a conserved and hydrophobic motif GLPLAL, a kinase-2a motif (LLVLDDV, when replaced by IAVFDDI in PAKRGA1 and a kinase-3a (FGPGSRIII were presented in all RGA. A phylogenetic tree, based on the deduced amino-acid sequences of PAKRGA1 and RGAs from different species indicated that they were separated in two clusters, PAKRGA1 being on cluster II. The isolated NBS analogs can be eventually used as guidelines to isolate numerous R-genes in Pistachio.

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

    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).


    Leonardo Aguiar Trujillo


    Full Text Available The orange processing industry generates high volumes of solid residue. This residue has been used in animal feeding and biochemical processes. A possible energy use of the waste can be thermochemical fast pyrolysis process. The objective was to determine the influence of the heating rate and temperature in the process of rapid pyrolysis of orange solid residue. In the process a design, 2k full factorial experiment was used, evaluating the influence of the independent variables and its interactions on the answers, using a 95 % significance level. We found that temperature is the most significant influence on the responses parameter having significant influence on the yields to: gas, coal, tar and the calorific value of the gas and the heating rate does not influence the answers. Finally, the interaction affects the gas yield. The results obtained in this study are: Rgas (19 – 38 %, Rchar (25 – 42 %, Ralq (6 – 12 %, PCIgas entre (140 – 1050 kJ/m3N.

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

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


    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. Remote geologic structural analysis of Yucca Flat

    Foley, M.G.; Heasler, P.G.; Hoover, K.A. [Pacific Northwest Lab., Richland, WA (United States); Rynes, N.J. [Northern Illinois Univ., De Kalb, IL (United States); Thiessen, R.L.; Alfaro, J.L. [Washington State Univ., Pullman, WA (United States)


    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.

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

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


    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.

  18. Isolation and Sequence Analysis of NBS-type Resistance gene Analogues from Hainan Common Wild Rice(Oryza rufipogon Griff)%海南普通野生稻NBS类抗病基因同源序列的分离与分析

    徐靖; 云勇; 唐清杰; 王效宁


    为研究海南普通野生稻中的STK类抗病基因,根据已知植物抗病基因NBS(Nucleotide binding site)序列中的保守区域设计简并引物,以海南普通野生稻基因组DNA为模板扩增得到4条具有连续ORF的抗病基因类似物(Resistance gene analogues,RGAs)序列,它们核苷酸序列间的相似性系数在53.14%-99.81%之间,而相应推测的氨基酸序列间的相似性系数在39.08%-99.42%之间.对氨基酸序列进行结构分析表明,它们包括"P-100p"、"Kinase-2a"、"Kinase-3a"和"GLPL"4个抗病基因所共有的保守模体,并且4条海南普通野生稻NBS-LRR类似物均属于nonTIR-NBS类抗病基因片段.

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

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


    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.

  20. Cloning and Characterization of Full Length cDNA of a CC-NBS-LRR Resistance Gene in Sweetpotato

    CHEN Guan-shui; ZHOU Yi-fei; HOU Li-li; PAN Da-ren


    Conserved domain such as nucleotide binding site (NBS) was found in several cloned plant disease resistance genes.Based on the NBS domain,resistance gene analogues (RGAs) have been isolated.A full-length cDNA,SPRI was obtained by rapid amplification of cDNA ends (RACE) method.Sequence analysis indicated that the length of SPR1 was 3 066 bp,including a complete open reading frame of 2 667 bp encoding SPRI protein of 888 amino acids.Compared with known NBS-LRR genes,it presented relatively high amino acid sequence identity.The polypeptide has a typical structure of non TIR-NBS-LRR genes,with NB-ARC,CC,and LRR domains.The SPR1-related sequences belonged to multicopy gene family in sweetpotato genome according to the result of Southern blotting.Semi-quantitative RT-PCR analysis showed SPR1 expressed in all tested tissues.The cloning of putative resistance gene from sweetpotato provides a basis for studying the structure and function of sweetpotato disease-resistance relating genes and disease resistant genetic breeding in sweetpotato.The gene has been submitted to the GenBank database,and the accession number is EF428453.

  1. Isolation and Identification of NBS-LRR Resistance Gene Analogs Sequences from Vitis davidii%中国野生刺葡萄抗白腐病NBS-LRR类抗病基因同源序列的分离与鉴定

    张颖; 李峰; 刘崇怀; 樊秀彩; 孙海生; 姜建福; 张国海


    [目的]通过同源克隆法从刺葡萄‘高山2号’叶片中得到抗白腐病基因的同源片段,为筛选葡萄抗白腐病基因奠定基础.[方法]根据已知植物抗病基因NBS-LRR保守区设计简并引物,从高抗葡萄白腐病刺葡萄‘高山2号’的基因组DNA与cDNA上得到抗病基因同源片段(RGAs),并对其表达分析进行检测.[结果]从刺葡萄‘高山2号’上获得了10个NBS-LRR类抗病基因同源片段,1 0条葡萄RGAs间在氨基酸水平上的同源性表现出丰富的多态性,进一步分析发现,在10条葡萄RGAs中,4个推测所属基因为non-TIR-NBS-LRR类抗病基因,6个所属基因为TIR-NBS-LRR类抗病基因.定量PCR分析表明,NB7基因受到白腐菌的诱导,而且NB7基因在刺葡萄叶片中为低丰度表达,NBS6基因受到白腐菌的诱导后为下调表达.[结论]在刺葡萄上成功获得了抗病基因同源序列,通过荧光定量PCR分析发现,NB7基因与NBS6基因都受到白腐菌的诱导表达,为最终克隆得到葡萄抗白腐病基因奠定基础.%[Objective] The purpose of this study was to get white rot disease resistant homologous clips from Vitis davidii Vitis davidii cv.Gaoshan 2',which will provide an effective means for screening white rot disease resistant gene.[Method] According to the known plant resistance genes NBS-LRR conservative area,degenerate primers were designed and used to clone targeted resistance gene analogs using templates of genomic DNA and cDNA from white rot disease resistant variety of Vitis davidii Vitis davidii cv.Gaoshan 2'.Then the gene expression analysis was performed.[Result] Ten NBS-LRR kinds of resistance gene analogs from Vitis davidii ‘V iris davidii cv.Gaoshan 2’ were obtained,and their amino acid sequences showed rich polymorphism.Further analysis found that among the ten NBS sequences,four genes belong to non-TIR-NBS-LRR kind of resistance genes,six belong to TIR-NBS-LRR kind of resistance genes.Quantitative PCR analysis

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

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


    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

  3. Observations of the smoke plume from the December 2005 explosions and prolonged oil fire at Buncefield oil depot, southern UK and associated atmospheric changes

    Mather, T. A.; Harrison, R. G.; Tsanev, V. I.; Pyle, D. M.; Karumudi, M. L.; Bennett, A. J.; Sawyer, G. M.; Highwood, E. J.


    The explosions and subsequent fire at the Buncefield oil depot in December 2005 afforded a rare opportunity to study the atmospheric consequences of a major oil fire at close range, using ground-based remote sensing instruments. The fire burned 5.6 × 107kg of refined fuel (unleaded petrol, aviation fuel and diesel) over 3 days and produced a plume of smoke that extended over much of southern England. Near-source measurements suggest that plume particles were ~50% black carbon (BC) with refractive index 1.73-0.42i, effective radius (Reff) 0.45-0.85μm and mass loading ~2000μg.m-3. About 50km downwind, particles were ~60-75% BC with refractive index between 1.80-0.52i and 1.89-0.69i, Reff ~1.0μm and mass loadings 320-780μg.m-3. Number distributions were almost all monomodal with peak at rgas concentrations of SO2 (70ppb), NO2 (140ppb), HONO (20ppb), HCHO (160ppb) and CS2 (40ppb). We estimate that the Buncefield event emitted totals of ~6.3, 7.2 and 5.5Mg of SO2, HCHO and CS2 respectively; along with ~5500Mg of BC. Our measurements are consistent with others of the Buncefield plume, and with studies of the 1991 Kuwaiti oil-fire plumes; differences from the latter reflecting in part a contrast in source composition (refined fuels vs. crude oils) leading to important potential differences in atmospheric impacts. Measurements made as the plume passed overhead ~50km downwind showed a reduced solar flux reaching the surface but little effect on the atmospheric potential gradient. The wind speed data from the day of the explosion hints at a possible explosion signature.

  4. Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes.

    Coyne, C J; McClendon, M T; Walling, J G; Timmerman-Vaughan, G M; Murray, S; Meksem, K; Lightfoot, D A; Shultz, J L; Keller, K E; Martin, R R; Inglis, D A; Rajesh, P N; McPhee, K E; Weeden, N F; Grusak, M A; Li, C-M; Storlie, E W


    Pea (Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2-0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.

  5. Isolation of Resistance Gene Candidates (RGCs) and characterization of an RGC cluster in cassava.

    López, C E; Zuluaga, A P; Cooke, R; Delseny, M; Tohme, J; Verdier, V


    Plant disease resistance genes (R genes) show significant similarity amongst themselves in terms of both their DNA sequences and structural motifs present in their protein products. Oligonucleotide primers designed from NBS (Nucleotide Binding Site) domains encoded by several R-genes have been used to amplify NBS sequences from the genomic DNA of various plant species, which have been called Resistance Gene Analogues (RGAs) or Resistance Gene Candidates (RGCs). Using specific primers from the NBS and TIR (Toll/Interleukin-1 Receptor) regions, we identified twelve classes of RGCs in cassava (Manihot esculenta Crantz). Two classes were obtained from the PCR-amplification of the TIR domain. The other 10 classes correspond to the NBS sequences and were grouped into two subfamilies. Classes RCa1 to RCa5 are part of the first subfamily and were linked to a TIR domain in the N terminus. Classes RCa6 to RCa10 corresponded to non-TIR NBS-LRR encoding sequences. BAC library screening with the 12 RGC classes as probes allowed the identification of 42 BAC clones that were assembled into 10 contigs and 19 singletons. Members of the two TIR and non-TIR NBS-LRR subfamilies occurred together within individual BAC clones. The BAC screening and Southern hybridization analyses showed that all RGCs were single copy sequences except RCa6 that represented a large and diverse gene family. One BAC contained five NBS sequences and sequence analysis allowed the identification of two complete RGCs encoding two highly similar proteins. This BAC was located on linkage group J with three other RGC-containing BACs. At least one of these genes, RGC2, is expressed constitutively in cassava tissues.

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

    Kristie L Connolly

    Full Text Available 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.

  7. The heat capacity of hydrous cordierite above 295 K

    Carey, J. William


    The heat capacity of synthetic hydrous cordierite (Mg2Al4Si5O18·nH2O) has been determined by differential scanning calorimetry (DSC) from 295 to 425 K as a function of H2O content. Six samples with H2O contents ranging from 0 to 0.82 per formula unit were examined. The partial molar heat capacity of H2O in cordierite over the measured temperature interval is independent of composition and temperature within experimental uncertainty and is equal to 43.3 ±0.8 J/mol/ K. This value exceeds the molar heat capacity of gaseous H2O by 9.7 J/mol/K, but is significantly smaller than the heat capacity of H2O in several zeolites and liquid H2O. A statistical-mechanical model of the heat capacity of adsorbed gas species (Barrer 1978) is used to extrapolate the heat capacity of hydrous cordierite to temperatures greater than 425 K. In this model, the heat capacity of hydrous cordierite (Crd·nH2O) is represented as follows: Cp(Crd · nH2O) = Cp(Crd)+ n{Cp(H2O, gas)+ R(gas constant)} (1) An examination of calorimetric data for hydrous beryl, analcime, mordenite, and clinoptilolite (Hemingway et al. 1986; Johnson et al. 1982, 1991, 1992) demonstrates the general applicability of the statistical-mechanical model for the extrapolation of heat capacity data of zeolitic minerals. The heat capacity data for cordierite are combined with the data of Carey and Navrotsky (1992) to obtain the molar enthalpy of formation and enthalpy of hydration of hydrous cordierite as a function of temperature.

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

    Oliver Richard P


    Full Text Available Abstract Background Knowledge of the genetic basis of plant resistance to necrotrophic pathogens is incomplete and has been characterised in relatively few pathosystems. In this study, the cytology and genetics of resistance to spring black stem and leaf spot caused by Phoma medicaginis, an economically important necrotrophic pathogen of Medicago spp., was examined in the model legume M. truncatula. Results Macroscopically, the resistant response of accession SA27063 was characterised by small, hypersensitive-like spots following inoculation while the susceptible interaction with accessions A17 and SA3054 showed necrotic lesions and spreading chlorosis. No unique cytological differences were observed during early infection (2 populations segregating for resistance to spring black stem and leaf spot were established between SA27063 and the two susceptible accessions, A17 and SA3054. The cross between SA27063 and A17 represented a wider cross than between SA27063 and SA3054, as evidenced by higher genetic polymorphism, reduced fertility and aberrant phenotypes of F2 progeny. In the SA27063 × A17 F2 population a highly significant quantitative trait locus (QTL, LOD = 7.37; P Phoma medicaginis one (rnpm1 genetically mapped to the top arm of linkage group 4 (LG4. rnpm1 explained 33.6% of the phenotypic variance in the population's response to infection depicted on a 1–5 scale and was tightly linked to marker AW256637. A second highly significant QTL (LOD = 6.77; P rnpm2, was located on the lower arm of LG8 in the SA27063 × SA3054 map. rnpm2 explained 29.6% of the phenotypic variance and was fine mapped to a 0.8 cM interval between markers h2_16a6a and h2_21h11d. rnpm1 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

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

    Frizzell, Caroline [Institute for Global Food Security, School of Biological Sciences, Queen' s University Belfast, Northern Ireland (United Kingdom); Ndossi, Doreen [Section of Experimental Biomedicine, Norwegian School of Veterinary Science, Oslo (Norway); Sokoine University of Agriculture, Morogoro (Tanzania, United Republic of); Kalayou, Shewit [Section of Experimental Biomedicine, Norwegian School of Veterinary Science, Oslo (Norway); Mekelle University College of Veterinary Medicine, Mekelle (Ethiopia); Eriksen, Gunnar S. [Norwegian Veterinary Institute, Oslo (Norway); Verhaegen, Steven [Section of Experimental Biomedicine, Norwegian School of Veterinary Science, Oslo (Norway); Sørlie, Morten [Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås (Norway); Elliott, Christopher T. [Institute for Global Food Security, School of Biological Sciences, Queen' s University Belfast, Northern Ireland (United Kingdom); Ropstad, Erik [Section of Experimental Biomedicine, Norwegian School of Veterinary Science, Oslo (Norway); Connolly, Lisa, E-mail: [Institute for Global Food Security, School of Biological Sciences, Queen' s University Belfast, Northern Ireland (United Kingdom)


    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.

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

    Guimarães Patricia M


    Full Text Available Abstract 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

  11. Identification and characterization of potential NBS-encoding resistance genes and induction kinetics of a putative candidate gene associated with downy mildew resistance in Cucumis

    Wan Hongjian


    Full Text Available Abstract Background Due to the variation and mutation of the races of Pseudoperonospora cubensis, downy mildew has in recent years become the most devastating leaf disease of cucumber worldwide. Novel resistance to downy mildew has been identified in the wild Cucumis species, C. hystrix Chakr. After the successful hybridization between C. hystrix and cultivated cucumber (C. sativus L., an introgression line (IL5211S was identified as highly resistant to downy mildew. Nucleotide-binding site and leucine-rich repeat (NBS-LRR genes are the largest class of disease resistance genes cloned from plant with highly conserved domains, which can be used to facilitate the isolation of candidate genes associated with downy mildew resistance in IL5211S. Results Degenerate primers that were designed based on the conserved motifs in the NBS domain of resistance (R proteins were used to isolate NBS-type sequences from IL5211S. A total of 28 sequences were identified and named as cucumber (C. sativus = CS resistance gene analogs as CSRGAs. Polygenetic analyses separated these sequences into four different classes. Quantitative real-time polymerase chain reaction (qRT-PCR analysis showed that these CSRGAs expressed at different levels in leaves, roots, and stems. In addition, introgression from C. hystrix induced expression of the partial CSRGAs in cultivated cucumber, especially CSRGA23, increased four-fold when compared to the backcross parent CC3. Furthermore, the expression of CSRGA23 under P. cubensis infection and abiotic stresses was also analyzed at different time points. Results showed that the P. cubensis treatment and four tested abiotic stimuli, MeJA, SA, ABA, and H2O2, triggered a significant induction of CSRGA23 within 72 h of inoculation. The results indicate that CSRGA23 may play a critical role in protecting cucumber against P. cubensis through a signaling the pathway triggered by these molecules. Conclusions Four classes of NBS-type RGAs were

  12. Axl signaling induces development of natural killer cells in vitro and in vivo.

    Kim, Eun-Mi; Lee, Eun-Hee; Lee, Hwa-Yeon; Choi, Ha-Rim; Ji, Kon-Young; Kim, Su-Man; Kim, Kwang Dong; Kang, Hyung-Sik


    Natural killer (NK) cells have been well known to play a critical role in innate immunity, but they are also capable of regulating adaptive immunity through the induction of T cell-mediated memory response and B cell-mediated autoimmune response. NK cells are differentiated from hematopoietic stem cells (HSCs) in the bone marrow (BM), and a series of surface molecules are expressed on NK cells in a differentiation stage-specific manner. Axl receptor tyrosine kinase is originally identified as homeostatic regulators for antigen-presenting cells, and its ligand, growth-arrest-specific gene 6 (Gas6), has been reported to promote cell survival, proliferation, and migration, but their regulatory role in the development and effector function of NK cells is not yet fully understood. In this study, to investigate whether Axl is required for the regulation of NK cell development, the expression of mature NK (mNK) cell-specific receptors and NK cell-associated genes was analyzed in the differentiated HSCs-derived NK cells in vitro and the NK cells harvested from Axl(-/-) mice. We found that agonistic anti-Axl antibody or recombinant Gas6 specifically upregulated the expression of mNK cell-specific receptors, such as LY49A, Ly49G2, Ly49C/F/I, NKG2A/C/E (1.5- to 3.5-fold increase), and NK cell-associated genes, such as IL-2Rβ (2.3- or 2.4-fold increase), Perforin (4.1- or 2.1-fold increase), IL-15Rα (2.14- or 2.04-fold increase), and IFN-γ (3.3- or 2.8-fold increase) compared to each isotype control, whereas it was abrogated by treatment of Axl-Ig. Anti-Axl antibody or rGas6 also induced a 2.5- or 1.9-fold increase in the proliferation of developing NK cells compared to each control, respectively. mNK cell populations expressing mNK cell-specific receptors were reduced about twofold in NK cells differentiated from HSCs of Axl(-/-) mice compared with those of wild-type mice. Furthermore, the triggering of Axl signaling by agonistic anti-Axl antibody promoted the

  13. Cloning and analysis on homologous sequences of STK-like R-gene from Cucumis melo%甜瓜STK类R基因同源序列的克隆与分析

    张志忠; 孙志浩; 蓝茂锋


    from Ricinus communis L. The alignment result of amino acid sequences reveals that tg2, tg5, tg9 and tgl 2 all contain nine conserved domains of ft-gene, which are candidate analog sequences of STK-like disease resistance genes. The molecular phylogenetic tree shows that tg2, tg5, tg9 and tgl2 only have 33.5%-53. 4% similarity in amino acid level with known R-genes (Pto, LrlO and Lectin) , and also there is low amino acid similarity among four homologous sequences of C. Melo, meaning that RGAs markers of C. melo may have high specificity.