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Sample records for rhizobial nodulation factors

  1. Coordinating nodule morphogenesis with rhizobial infection in legumes.

    PubMed

    Oldroyd, Giles E D; Downie, J Allan

    2008-01-01

    The formation of nitrogen-fixing nodules on legumes requires an integration of infection by rhizobia at the root epidermis and the initiation of cell division in the cortex, several cell layers away from the sites of infection. Several recent developments have added to our understanding of the signaling events in the epidermis associated with the perception of rhizobial nodulation factors and the role of plant hormones in the activation of cell division leading to nodule morphogenesis. This review focuses on the tissue-specific nature of the developmental processes associated with nodulation and the mechanisms by which these processes are coordinated during the formation of a nodule. PMID:18444906

  2. Rhizobial gibberellin negatively regulates host nodule number.

    PubMed

    Tatsukami, Yohei; Ueda, Mitsuyoshi

    2016-01-01

    In legume-rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. In Lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. However, we have discovered a symbiont-derived phytohormonal regulation of nodule number in Mesorhizobium loti. In this study, we found that M. loti synthesized gibberellic acid (GA) under symbiosis. Hosts inoculated with a GA-synthesis-deficient M. loti mutant formed more nodules than those inoculated with the wild-type form at four weeks post inoculation, indicating that GA from already-incorporated rhizobia prevents new nodule formation. Interestingly, the genes for GA synthesis are only found in rhizobial species that inhabit determinate nodules. Our findings suggest that the already-incorporated rhizobia perform GA-associated negative regulation of nodule number to prevent delayed infection by other rhizobia. PMID:27307029

  3. Rhizobial gibberellin negatively regulates host nodule number

    PubMed Central

    Tatsukami, Yohei; Ueda, Mitsuyoshi

    2016-01-01

    In legume–rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. In Lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. However, we have discovered a symbiont-derived phytohormonal regulation of nodule number in Mesorhizobium loti. In this study, we found that M. loti synthesized gibberellic acid (GA) under symbiosis. Hosts inoculated with a GA-synthesis-deficient M. loti mutant formed more nodules than those inoculated with the wild-type form at four weeks post inoculation, indicating that GA from already-incorporated rhizobia prevents new nodule formation. Interestingly, the genes for GA synthesis are only found in rhizobial species that inhabit determinate nodules. Our findings suggest that the already-incorporated rhizobia perform GA-associated negative regulation of nodule number to prevent delayed infection by other rhizobia. PMID:27307029

  4. The Symbiosis-Related ERN Transcription Factors Act in Concert to Coordinate Rhizobial Host Root Infection.

    PubMed

    Cerri, Marion R; Frances, Lisa; Kelner, Audrey; Fournier, Joëlle; Middleton, Patrick H; Auriac, Marie-Christine; Mysore, Kirankumar S; Wen, Jiangqi; Erard, Monique; Barker, David G; Oldroyd, Giles E; de Carvalho-Niebel, Fernanda

    2016-06-01

    Legumes improve their mineral nutrition through nitrogen-fixing root nodule symbioses with soil rhizobia. Rhizobial infection of legumes is regulated by a number of transcription factors, including ERF Required for Nodulation1 (ERN1). Medicago truncatula plants defective in ERN1 are unable to nodulate, but still exhibit early symbiotic responses including rhizobial infection. ERN1 has a close homolog, ERN2, which shows partially overlapping expression patterns. Here we show that ern2 mutants exhibit a later nodulation phenotype than ern1, being able to form nodules but with signs of premature senescence. Molecular characterization of the ern2-1 mutation reveals a key role for a conserved threonine for both DNA binding and transcriptional activity. In contrast to either single mutant, the double ern1-1 ern2-1 line is completely unable to initiate infection or nodule development. The strong ern1-1 ern2-1 phenotype demonstrates functional redundancy between these two transcriptional regulators and reveals the essential role of ERN1/ERN2 to coordinately induce rhizobial infection and nodule organogenesis. While ERN1/ERN2 act in concert in the root epidermis, only ERN1 can efficiently allow the development of mature nodules in the cortex, probably through an independent pathway. Together, these findings reveal the key roles that ERN1/ERN2 play at the very earliest stages of root nodule development. PMID:27208242

  5. DELLA-mediated gibberellin signalling regulates Nod factor signalling and rhizobial infection.

    PubMed

    Fonouni-Farde, Camille; Tan, Sovanna; Baudin, Maël; Brault, Mathias; Wen, Jiangqi; Mysore, Kirankumar S; Niebel, Andreas; Frugier, Florian; Diet, Anouck

    2016-01-01

    Legumes develop symbiotic interactions with rhizobial bacteria to form nitrogen-fixing nodules. Bacterial Nod factors (NFs) and plant regulatory pathways modulating NF signalling control rhizobial infections and nodulation efficiency. Here we show that gibberellin (GA) signalling mediated by DELLA proteins inhibits rhizobial infections and controls the NF induction of the infection marker ENOD11 in Medicago truncatula. Ectopic expression of a constitutively active DELLA protein in the epidermis is sufficient to promote ENOD11 expression in the absence of symbiotic signals. We show using heterologous systems that DELLA proteins can interact with the nodulation signalling pathway 2 (NSP2) and nuclear factor-YA1 (NF-YA1) transcription factors that are essential for the activation of NF responses. Furthermore, MtDELLA1 can bind the ERN1 (ERF required for nodulation 1) promoter and positively transactivate its expression. Overall, we propose that GA-dependent action of DELLA proteins may directly regulate the NSP1/NSP2 and NF-YA1 activation of ERN1 transcription to regulate rhizobial infections. PMID:27586842

  6. NODULES WITH ACTIVATED DEFENSE 1 is required for maintenance of rhizobial endosymbiosis in Medicago truncatula.

    PubMed

    Wang, Chao; Yu, Haixiang; Luo, Li; Duan, Liujian; Cai, Liuyang; He, Xinxing; Wen, Jiangqi; Mysore, Kirankumar S; Li, Guoliang; Xiao, Aifang; Duanmu, Deqiang; Cao, Yangrong; Hong, Zonglie; Zhang, Zhongming

    2016-10-01

    The symbiotic interaction between legume plants and rhizobia results in the formation of root nodules, in which symbiotic plant cells host and harbor thousands of nitrogen-fixing rhizobia. Here, a Medicago truncatula nodules with activated defense 1 (nad1) mutant was identified using reverse genetics methods. The mutant phenotype was characterized using cell and molecular biology approaches. An RNA-sequencing technique was used to analyze the transcriptomic reprogramming of nad1 mutant nodules. In the nad1 mutant plants, rhizobial infection and propagation in infection threads are normal, whereas rhizobia and their symbiotic plant cells become necrotic immediately after rhizobia are released from infection threads into symbiotic cells of nodules. Defense-associated responses were detected in nad1 nodules. NAD1 is specifically present in root nodule symbiosis plants with the exception of Morus notabilis, and the transcript is highly induced in nodules. NAD1 encodes a small uncharacterized protein with two predicted transmembrane helices and is localized at the endoplasmic reticulum. Our data demonstrate a positive role for NAD1 in the maintenance of rhizobial endosymbiosis during nodulation. PMID:27245091

  7. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory NolR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory...

  8. The Symbiosis-Related ERN Transcription Factors Act in Concert to Coordinate Rhizobial Host Root Infection1[OPEN

    PubMed Central

    Cerri, Marion R.; Frances, Lisa; Kelner, Audrey; Middleton, Patrick H.; Auriac, Marie-Christine; Mysore, Kirankumar S.; Erard, Monique; Barker, David G.

    2016-01-01

    Legumes improve their mineral nutrition through nitrogen-fixing root nodule symbioses with soil rhizobia. Rhizobial infection of legumes is regulated by a number of transcription factors, including ERF Required for Nodulation1 (ERN1). Medicago truncatula plants defective in ERN1 are unable to nodulate, but still exhibit early symbiotic responses including rhizobial infection. ERN1 has a close homolog, ERN2, which shows partially overlapping expression patterns. Here we show that ern2 mutants exhibit a later nodulation phenotype than ern1, being able to form nodules but with signs of premature senescence. Molecular characterization of the ern2-1 mutation reveals a key role for a conserved threonine for both DNA binding and transcriptional activity. In contrast to either single mutant, the double ern1-1 ern2-1 line is completely unable to initiate infection or nodule development. The strong ern1-1 ern2-1 phenotype demonstrates functional redundancy between these two transcriptional regulators and reveals the essential role of ERN1/ERN2 to coordinately induce rhizobial infection and nodule organogenesis. While ERN1/ERN2 act in concert in the root epidermis, only ERN1 can efficiently allow the development of mature nodules in the cortex, probably through an independent pathway. Together, these findings reveal the key roles that ERN1/ERN2 play at the very earliest stages of root nodule development. PMID:27208242

  9. Phylogenetic diversity of rhizobial species and symbiovars nodulating Phaseolus vulgaris in Iran.

    PubMed

    Rouhrazi, Kiomars; Khodakaramian, Gholam; Velázquez, Encarna

    2016-03-01

    The phylogenetic diversity of 29 rhizobial strains nodulating Phaseolus vulgaris in Iran was analysed on the basis of their core and symbiotic genes. These strains displayed five 16S rRNA-RFLP patterns and belong to eight ERIC-PCR clusters. The phylogenetic analyses of 16S rRNA, recA and atpD core genes allowed the identification of several strains as Rhizobium sophoriradicis, R. leguminosarum, R. tropici and Pararhizobium giardinii, whereas other strains represented a new phylogenetic lineage related to R. vallis. These strains and those identified as R. sophoriradicis and R. leguminosarum belong to the symbiovar phaseoli carrying the γ nodC allele distributed in P. vulgaris endosymbionts in America, Europe, Africa and Asia. The strain identified as R. tropici belongs to the symbiovar tropici carried by strains of R. tropici, R. leucaenae, R. lusitanum and R. freirei nodulating P. vulgaris in America, Africa and Asia. The strain identified as P. giardinii belongs to the symbiovar giardinii together with the type strain of this species nodulating P. vulgaris in France. It is remarkable that the recently described species R. sophoriradicis is worldwide distributed in P. vulgaris nodules carrying the γ nodC allele of symbiovar phaseoli harboured by rhizobia isolated in the American distribution centers of this legume. PMID:26832644

  10. Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes.

    PubMed

    Laguerre, Gisèle; Louvrier, Philippe; Allard, Marie-Reine; Amarger, Noëlle

    2003-04-01

    Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy. PMID:12676710

  11. Diversity patterns of Rhizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes.

    PubMed

    Miranda-Sánchez, Fabiola; Rivera, Javier; Vinuesa, Pablo

    2016-09-01

    Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyse alpha and beta diversity patterns of Rhizobiaceae communities from a conserved seasonally dry tropical forest site in central Mexico and two nearby agricultural fields. Lineage-specific recA amplicon libraries were generated from soil DNA and their sequences compared with those from root surface and nodule isolates recovered in trapping experiments from two native Acacia species and two Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A 'rare biosphere'-like distribution of species was found in the three habitats. Multivariate statistical analyses demonstrated that the plant genus exerted a stronger influence than the land-usage regime on the diversity of rhizobia associated with hosts. Rhizobium etli was the dominant Rhizobiaceae found in the soil libraries. It dominated nodulation of Acacia spp. and predominately harboured symbiovar mimosae-like nodC genes. A novel Rhizobium lineage (Rsp1) dominated bean nodulation. Specialist and generalist genotypes for host nodulation were detected in both species. PMID:26395550

  12. Biosynthesis of compatible solutes in rhizobial strains isolated from Phaseolus vulgaris nodules in Tunisian fields

    PubMed Central

    2010-01-01

    Background Associated with appropriate crop and soil management, inoculation of legumes with microbial biofertilizers can improve food legume yield and soil fertility and reduce pollution by inorganic fertilizers. Rhizospheric bacteria are subjected to osmotic stress imposed by drought and/or NaCl, two abiotic constraints frequently found in semi-arid lands. Osmostress response in bacteria involves the accumulation of small organic compounds called compatible solutes. Whereas most studies on rhizobial osmoadaptation have focussed on the model species Sinorhizobium meliloti, little is known on the osmoadaptive mechanisms used by native rhizobia, which are good sources of inoculants. In this work, we investigated the synthesis and accumulations of compatible solutes by four rhizobial strains isolated from root nodules of Phaseolus vulgaris in Tunisia, as well as by the reference strain Rhizobium tropici CIAT 899T. Results The most NaCl-tolerant strain was A. tumefaciens 10c2, followed (in decreasing order) by R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3, R. etli 12a3 and R. gallicum bv. phaseoli 8a3. 13C- and 1H-NMR analyses showed that all Rhizobium strains synthesized trehalose whereas A. tumefaciens 10c2 synthesized mannosucrose. Glutamate synthesis was also observed in R. tropici CIAT 899, R. leguminosarum bv. phaseoli 31c3 and A. tumefaciens 10c2. When added as a carbon source, mannitol was also accumulated by all strains. Accumulation of trehalose in R. tropici CIAT 899 and of mannosucrose in A. tumefaciens 10c2 was osmoregulated, suggesting their involvement in osmotolerance. The phylogenetic analysis of the otsA gene, encoding the trehalose-6-phosphate synthase, suggested the existence of lateral transfer events. In vivo 13C labeling experiments together with genomic analysis led us to propose the uptake and conversion pathways of different carbon sources into trehalose. Collaterally, the β-1,2-cyclic glucan from R. tropici CIAT 899 was co

  13. Impact of the energy crop Jatropha curcas L. on the composition of rhizobial populations nodulating cowpea (Vigna unguiculata L.) and acacia (Acacia seyal L.).

    PubMed

    Dieng, Amadou; Duponnois, Robin; Floury, Antoine; Laguerre, Gisèle; Ndoye, Ibrahima; Baudoin, Ezékiel

    2015-03-01

    Jatropha curcas, a Euphorbiaceae species that produces many toxicants, is increasingly planted as an agrofuel plant in Senegal. The purpose of this study was to determine whether soil priming induced by J. curcas monoculture could alter the rhizobial populations that nodulate cowpea and acacia, two locally widespread legumes. Soil samples were transferred into a greenhouse from three fields previously cultivated with Jatropha for 1, 2, and 15 years, and the two trap legumes were grown in them. Control soil samples were also taken from adjacent Jatropha-fallow plots. Both legumes tended to develop fewer but larger nodules when grown in Jatropha soils. Nearly all the nifH sequences amplified from nodule DNA were affiliated to the Bradyrhizobium genus. Only sequences from Acacia seyal nodules grown in the most recent Jatropha plantation were related to the Mesorhizobium genus, which was much a more conventional finding on A. seyal than the unexpected Bradyrhizobium genus. Apart from this particular case, only minor differences were found in the respective compositions of Jatropha soil versus control soil rhizobial populations. Lastly, the structure of these rhizobial populations was systematically imbalanced owing to the overwhelming dominance of a very small number of nifH genotypes, some of which were identical across soil types or even sites. Despite these weak and sparse effects on rhizobial diversity, future investigations should focus on the characterization of the nitrogen-fixing abilities of the predominant rhizobial strains. PMID:25466917

  14. Into the Root: How Cytokinin Controls Rhizobial Infection.

    PubMed

    Miri, Mandana; Janakirama, Preetam; Held, Mark; Ross, Loretta; Szczyglowski, Krzysztof

    2016-03-01

    Leguminous plants selectively initiate primary responses to rhizobial nodulation factors (NF) that ultimately lead to symbiotic root nodule formation. Functioning downstream, cytokinin has emerged as the key endogenous plant signal for nodule differentiation, but its role in mediating rhizobial entry into the root remains obscure. Nonetheless, such a role is suggested by aberrant infection phenotypes of plant mutants with defects in cytokinin signaling. We postulate that cytokinin participates in orchestrating signaling events that promote rhizobial colonization of the root cortex and limit the extent of subsequent infection at the root epidermis, thus maintaining homeostasis of the symbiotic interaction. We further argue that cytokinin signaling must have been crucial during the evolution of plant cell predisposition for rhizobial colonization. PMID:26459665

  15. Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti

    PubMed Central

    Jones, Kathryn M.

    2013-01-01

    Rhizobial bacteria form symbiotic, nitrogen-fixing nodules on the roots of compatible host legume plants. One of the most well-developed model systems for studying these interactions is the plant Medicago truncatula cv. Jemalong A17 and the rhizobial bacterium Sinorhizobium meliloti 1021. Repeated imaging of plant roots and scoring of symbiotic phenotypes requires methods that are non-destructive to either plants or bacteria. The symbiotic phenotypes of some plant and bacterial mutants become apparent after relatively short periods of growth, and do not require long-term observation of the host/symbiont interaction. However, subtle differences in symbiotic efficiency and nodule senescence phenotypes that are not apparent in the early stages of the nodulation process require relatively long growth periods before they can be scored. Several methods have been developed for long-term growth and observation of this host/symbiont pair. However, many of these methods require repeated watering, which increases the possibility of contamination by other microbes. Other methods require a relatively large space for growth of large numbers of plants. The method described here, symbiotic growth of M. truncatula/S. meliloti in sterile, single-plant microcosms, has several advantages. Plants in these microcosms have sufficient moisture and nutrients to ensure that watering is not required for up to 9 weeks, preventing cross-contamination during watering. This allows phenotypes to be quantified that might be missed in short-term growth systems, such as subtle delays in nodule development and early nodule senescence. Also, the roots and nodules in the microcosm are easily viewed through the plate lid, so up-rooting of the plants for observation is not required. PMID:24121837

  16. Lotus endemic to the Canary Islands are nodulated by diverse and novel rhizobial species and symbiotypes.

    PubMed

    Lorite, Ma José; Donate-Correa, Javier; del Arco-Aguilar, Marcelino; Pérez Galdona, Ricardo; Sanjuán, Juan; León-Barrios, Milagros

    2010-08-01

    Genetic and symbiotic characterization of 34 isolates from several Lotus species endemic to the Canary Islands showed extraordinary diversity, with bacteria belonging to different species of the genera Mesorhizobium (17 isolates), Sinorhizobium (12 isolates) and Rhizobium/Agrobacterium (5 isolates). In a previous report, we showed that the Sinorhizobium isolates mostly belonged to S. meliloti. Here, we focused on the remaining isolates. The Lotus mesorhizobial strains were distributed in the rrs tree within six poorly resolved branches. Partial sequences from atpD and recA genes produced much better resolved phylogenies that were, with some exceptions, congruent with the ribosomal phylogeny. Thus, up to six different mesorhizobial species were detected, which matched with or were sister species of M. ciceri, M. alhagi, M. plurifarium or M. caraganae, and two represented new lineages that did not correspond to any of the currently recognized species. Neither M. loti nor Bradyrhizobium sp. (Lotus), recognized as the typical Lotus-symbionts, were identified among the Canarian Lotus isolates, although their nodulation genes were closely related to M. loti. However, several subbranches of mesorhizobia nodulating Lotus spp. could be differentiated in a nodC tree, with the isolates from the islands distributed in two of them (A1 and A3). Subbranch A1 included reference strains of M. loti and a group of isolates with a host range compatible with biovar loti, whereas A3 represented a more divergent exclusive subbranch of isolates with a host range almost restricted to endemic Lotus and it could represent a new biovar among the Lotus rhizobia. PMID:20447791

  17. Rhizobial strains isolated from nodules of Medicago marina in southwest Spain are abiotic-stress tolerant and symbiotically diverse.

    PubMed

    Alías-Villegas, Cynthia; Cubo, M Teresa; Lara-Dampier, Victoria; Bellogín, Ramón A; Camacho, María; Temprano, Francisco; Espuny, M Rosario

    2015-10-01

    The isolation and characterisation of nitrogen-fixing root nodule bacteria from Medicago marina, a tolerant legume species, were studied in two areas from southwest Spain. A total of 30 out of 82 isolates with distinct ERIC-PCR fingerprints were analysed on the basis of molecular (PCR-RFLP of the 16S-23S rDNA intergenic spacer region (IGS) with two endonucleases, analysis of the 16S rDNA and symbiotic nodC gene sequences, plasmid profiles and SDS-PAGE of LPS, including the partial sequence of the housekeeping gene glnII and the symbiotic gene nodA of some representatives), physiological (utilisation of sole carbon sources, tolerance to antibiotics, NaCl, heavy metals, temperature and pH) and symbiotic parameters (efficacy on M. marina, M. minima, M. murex, M. orbicularis, M. polymorpha, M. sativa and M. truncatula). All the bacteria isolated from M. marina nodules belonged to Ensifer meliloti, except for one strain that belonged to E. medicae. To determine the nodulation range of M. marina, 10 different Ensifer species were tested for their ability to nodulate on this plant. E. kummerowiae CCBAU 71714 and the E. medicae control strain M19.1 were the only Ensifer species tested that developed nitrogen-fixing nodules on this plant. Most of the M. marina-nodulating strains showed tolerance to stress factors and all of them shared the presence of a gene similar to cadA, a gene that encodes for a PIB-type ATPase, which is a transporter belonging to the large superfamily of ATP-driven pumps involved in the transport of metals across cell membranes. PMID:26299372

  18. Development of functional symbiotic white clover root hairs and nodules requires tightly regulated production of rhizobial cellulase CelC2.

    PubMed

    Robledo, Marta; Jiménez-Zurdo, José I; Soto, M José; Velázquez, Encarnación; Dazzo, Frank; Martínez-Molina, Eustoquio; Mateos, Pedro F

    2011-07-01

    The establishment of rhizobia as nitrogen-fixing endosymbionts within legume root nodules requires the disruption of the plant cell wall to breach the host barrier at strategic infection sites in the root hair tip and at points of bacterial release from infection threads (IT) within the root cortex. We previously found that Rhizobium leguminosarum bv. trifolii uses its chromosomally encoded CelC2 cellulase to erode the noncrystalline wall at the apex of root hairs, thereby creating the primary portal of its entry into white clover roots. Here, we show that a recombinant derivative of R. leguminosarum bv. trifolii ANU843 that constitutively overproduces the CelC2 enzyme has increased competitiveness in occupying aberrant nodule-like root structures on clover that are inefficient in nitrogen fixation. This aberrant symbiotic phenotype involves an extensive uncontrolled degradation of the host cell walls restricted to the expected infection sites at tips of deformed root hairs and significantly enlarged infection droplets at termini of wider IT within the nodule infection zone. Furthermore, signs of elevated plant host defense as indicated by reactive oxygen species production in root tissues were more evident during infection by the recombinant strain than its wild-type parent. Our data further support the role of the rhizobial CelC2 cell wall-degrading enzyme in primary infection, and show evidence of its importance in secondary symbiotic infection and tight regulation of its production to establish an effective nitrogen-fixing root nodule symbiosis. PMID:21405987

  19. Functional analysis of alternative transcripts of the soybean Rj2 gene that restricts nodulation with specific rhizobial strains.

    PubMed

    Tang, F; Yang, S; Zhu, H

    2016-05-01

    The Rj2 gene is a TIR-NBS-LRR-type resistance gene in soybean (Glycine max) that restricts root nodule symbiosis with a group of Bradyrhizobium japonicum strains including USDA122. Rj2 generates two distinct transcript variants in its expression profile through alternative splicing. Alternative splicing of Rj2 is caused by the retention of the 86-bp intron 4. Inclusion of intron 4 in mature mRNA introduces an in-frame stop codon; as such, the alternative transcript is predicted to encode a truncated protein consisting of the entire portion of the TIR, NBS and LRR domains but missing the C-terminal domain of the full-length Rj2 protein encoded by the regular transcript. Since alternative splicing has been shown to be essential for full activity of several plant R genes, we attempted to test whether the alternative splicing is required for Rj2-mediated nodulation restriction. Here we demonstrated that the Rj2-mediated nodulation restriction does not require the combined presence of the regular and alternative transcripts, and the expression of the regular transcript alone is sufficient to confer nodulation restriction. PMID:26848549

  20. Plant Hormonal Regulation of Nitrogen-Fixing Nodule Organogenesis

    PubMed Central

    Ryu, Hojin; Cho, Hyunwoo; Choi, Daeseok; Hwang, Ildoo

    2012-01-01

    Legumes have evolved symbiotic interactions with rhizobial bacteria to efficiently utilize nitrogen. Recent progress in symbiosis has revealed several key components of host plants required for nitrogen-fixing nodule organogenesis, in which complicated metabolic and signaling pathways in the host plant are reprogrammed to generate nodules in the cortex upon perception of the rhizobial Nod factor. Following the recognition of Nod factors, plant hormones are likely to be essential throughout nodule organogenesis for integration of developmental and environmental signaling cues into nodule development. Here, we review the molecular events involved in plant hormonal regulation and signaling cross-talk for nitrogen-fixing nodule development, and discuss how these signaling networks are integrated into Nod factor-mediated signaling during plant-microbe interactions. PMID:22820920

  1. Engineering Rhizobial Bioinoculants: A Strategy to Improve Iron Nutrition

    PubMed Central

    Geetha, S. J.; Joshi, Sanket J.

    2013-01-01

    Under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. In order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. Competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. Iron sufficiency is an important factor determining the survival and nodulation by rhizobia in soil. Siderophores, a class of ferric specific ligands that are involved in receptor specific iron transport into bacteria, constitute an important part of iron acquisition systems in rhizobia and have been shown to play a role in symbiosis as well as in saprophytic survival. Soils predominantly have iron bound to hydroxamate siderophores, a pool that is largely unavailable to catecholate-utilizing rhizobia. Outer membrane receptors for uptake of ferric hydroxamates include FhuA and FegA which are specific for ferrichrome siderophore. Increase in nodule occupancy and enhanced plant growth of the fegA and fhuA expressing engineered bioinoculants rhizobial strain have been reported. Engineering rhizobia for developing effective bioinoculants with improved ability to utilize heterologous siderophores could provide them with better iron acquisition ability and consequently, rhizospheric stability. PMID:24319357

  2. A Phylogenetically Conserved Group of Nuclear Factor-Y Transcription Factors Interact to Control Nodulation in Legumes1[OPEN

    PubMed Central

    Laloum, Tom; Lepage, Agnès; Ariel, Federico; Frances, Lisa; Gamas, Pascal; de Carvalho-Niebel, Fernanda

    2015-01-01

    The endosymbiotic association between legumes and soil bacteria called rhizobia leads to the formation of a new root-derived organ called the nodule in which differentiated bacteria convert atmospheric nitrogen into a form that can be assimilated by the host plant. Successful root infection by rhizobia and nodule organogenesis require the activation of symbiotic genes that are controlled by a set of transcription factors (TFs). We recently identified Medicago truncatula nuclear factor-YA1 (MtNF-YA1) and MtNF-YA2 as two M. truncatula TFs playing a central role during key steps of the Sinorhizobium meliloti-M. truncatula symbiotic interaction. NF-YA TFs interact with NF-YB and NF-YC subunits to regulate target genes containing the CCAAT box consensus sequence. In this study, using a yeast two-hybrid screen approach, we identified the NF-YB and NF-YC subunits able to interact with MtNF-YA1 and MtNF-YA2. In yeast (Saccharomyces cerevisiae) and in planta, we further demonstrated by both coimmunoprecipitation and bimolecular fluorescence complementation that these NF-YA, -B, and -C subunits interact and form a stable NF-Y heterotrimeric complex. Reverse genetic and chromatin immunoprecipitation-PCR approaches revealed the importance of these newly identified NF-YB and NF-YC subunits for rhizobial symbiosis and binding to the promoter of MtERN1 (for Ethylene Responsive factor required for Nodulation), a direct target gene of MtNF-YA1 and MtNF-YA2. Finally, we verified that a similar trimer is formed in planta by the common bean (Phaseolus vulgaris) NF-Y subunits, revealing the existence of evolutionary conserved NF-Y protein complexes to control nodulation in leguminous plants. This sheds light on the process whereby an ancient heterotrimeric TF mainly controlling cell division in animals has acquired specialized functions in plants. PMID:26432878

  3. Factors functioning in nodule melanization of insects and their mechanisms of accumulation in nodules.

    PubMed

    Tokura, Ai; Fu, Gege Sun; Sakamoto, Maki; Endo, Haruka; Tanaka, Shiho; Kikuta, Shingo; Tabunoki, Hiroko; Sato, Ryoichi

    2014-01-01

    Nodules consisting of hemocytes and trapped microorganisms are important targets for melanization, which is best known in the insect immune system. We investigated factors functioning in nodule melanization and the mechanism by which these factors congregate in the nodule. BmHP21, BmSPH1 and BmSPH2, Bombyx mori orthologs of Manduca sexta serine protease HP21, serine protease homologs (SPH1 and SPH2), and a prophenoloxidase, BmPO1 were observed as inactive forms in the plasma, but as putatively active forms in the nodule. Production of prophenoloxidase-activating proteinases, BmPAP1 and BmPAP3/PPAE and BmPO1 were confirmed in hemocytes. BmSPH1 and BmSPH2 were observed on trapped bacterial cells in the nodule and were isolated from the surface of bacterial cells incubated with plasma. BmSPH1 and BmSPH2 were found in plasma in complex with a pattern recognition receptor, BmLBP. These data suggest that melanization-regulating factors congregate in nodules through a combination of microorganism-dependent and hemocyte-dependent routes. PMID:24262307

  4. Dual involvement of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence.

    PubMed

    de Zélicourt, Axel; Diet, Anouck; Marion, Jessica; Laffont, Carole; Ariel, Federico; Moison, Michaël; Zahaf, Ons; Crespi, Martin; Gruber, Véronique; Frugier, Florian

    2012-04-01

    Legume crops related to the model plant Medicago truncatula can adapt their root architecture to environmental conditions, both by branching and by establishing a symbiosis with rhizobial bacteria to form nitrogen-fixing nodules. Soil salinity is a major abiotic stress affecting plant yield and root growth. Previous transcriptomic analyses identified several transcription factors linked to the M. truncatula response to salt stress in roots, including NAC (NAM/ATAF/CUC)-encoding genes. Over-expression of one of these transcription factors, MtNAC969, induced formation of a shorter and less-branched root system, whereas RNAi-mediated MtNAC969 inactivation promoted lateral root formation. The altered root system of over-expressing plants was able to maintain its growth under high salinity, and roots in which MtNAC969 was down-regulated showed improved growth under salt stress. Accordingly, expression of salt stress markers was decreased or induced in MtNAC969 over-expressing or RNAi roots, respectively, suggesting a repressive function for this transcription factor in the salt-stress response. Expression of MtNAC969 in central symbiotic nodule tissues was induced by nitrate treatment, and antagonistically affected by salt in roots and nodules, similarly to senescence markers. MtNAC969 RNAi nodules accumulated amyloplasts in the nitrogen-fixing zone, and were prematurely senescent. Therefore, the MtNAC969 transcription factor, which is differentially affected by environmental cues in root and nodules, participates in several pathways controlling adaptation of the M. truncatula root system to the environment. PMID:22098255

  5. Agro-industrial waste materials and wastewater sludge for rhizobial inoculant production: a review.

    PubMed

    Ben Rebah, F; Prévost, D; Yezza, A; Tyagi, R D

    2007-12-01

    Inoculating legumes with commercial rhizobial inoculants is a common agriculture practice. Generally, inoculants are sold in liquid or in solid forms (mixed with carrier). The production of inoculants involves a step in which a high number of cells are produced, followed by the product formulation. This process is largely governed by the cost related to the medium used for rhizobial growth and by the availability of a carrier source (peat) for production of solid inoculant. Some industrial and agricultural by-products (e.g. cheese whey, malt sprouts) contain growth factors such as nitrogen and carbon, which can support growth of rhizobia. Other agro-industrial wastes (e.g. plant compost, filtermud, fly-ash) can be used as a carrier for rhizobial inoculant. More recently, wastewater sludge, a worldwide recyclable waste, has shown good potential for inoculant production as a growth medium and as a carrier (dehydrated sludge). Sludge usually contains nutrient elements at concentrations sufficient to sustain rhizobial growth and heavy metals are usually below the recommended level. In some cases, growth conditions can be optimized by a sludge pre-treatment or by the addition of nutrients. Inoculants produced in wastewater sludge are efficient for nodulation and nitrogen fixation with legumes as compared to standard inoculants. This new approach described in this review offers a safe environmental alternative for both waste treatment/disposal and inoculant production. PMID:17336515

  6. Nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis.

    PubMed

    Mora, Yolanda; Díaz, Rafael; Vargas-Lagunas, Carmen; Peralta, Humberto; Guerrero, Gabriela; Aguilar, Alejandro; Encarnación, Sergio; Girard, Lourdes; Mora, Jaime

    2014-09-01

    Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the Rhizobium and Sinorhizobium groups. The strains showed several large plasmids, except for a Sinorhizobium americanum isolate. Two strains, one Rhizobium phaseoli and one S. americanum strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The S. americanum strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The R. phaseoli strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-β-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in Phaseolus seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains. PMID:25002426

  7. Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

    PubMed Central

    Mora, Yolanda; Díaz, Rafael; Vargas-Lagunas, Carmen; Peralta, Humberto; Guerrero, Gabriela; Aguilar, Alejandro; Encarnación, Sergio; Girard, Lourdes

    2014-01-01

    Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the Rhizobium and Sinorhizobium groups. The strains showed several large plasmids, except for a Sinorhizobium americanum isolate. Two strains, one Rhizobium phaseoli and one S. americanum strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The S. americanum strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The R. phaseoli strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-β-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in Phaseolus seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains. PMID:25002426

  8. Analysis of rhizobial strains nodulating Phaseolus vulgaris from Hispaniola Island, a geographic bridge between Meso and South America and the first historical link with Europe.

    PubMed

    Díaz-Alcántara, César-Antonio; Ramírez-Bahena, Martha-Helena; Mulas, Daniel; García-Fraile, Paula; Gómez-Moriano, Alicia; Peix, Alvaro; Velázquez, Encarna; González-Andrés, Fernando

    2014-03-01

    Hispaniola Island was the first stopover in the travels of Columbus between America and Spain, and played a crucial role in the exchange of Phaseolus vulgaris seeds and their endosymbionts. The analysis of recA and atpD genes from strains nodulating this legume in coastal and inner regions of Hispaniola Island showed that they were almost identical to those of the American strains CIAT 652, Ch24-10 and CNPAF512, which were initially named as Rhizobium etli and have been recently reclassified into Rhizobium phaseoli after the analysis of their genomes. Therefore, the species R. phaseoli is more abundant in America than previously thought, and since the proposal of the American origin of R. etli was based on the analysis of several strains that are currently known to be R. phaseoli, it can be concluded that both species have an American origin coevolving with their host in its distribution centres. The analysis of the symbiovar phaseoli nodC gene alleles carried by different species isolated in American and European countries suggested a Mesoamerican origin of the α allele and an Andean origin of the γ allele, which is supported by the dominance of this latter allele in Europe where mostly Andean cultivars of common beans have been traditionally cultivated. PMID:24239274

  9. Nodulation gene factors and plant response in the Rhizobium-legume symbiosis. [Nodulation

    SciTech Connect

    Long, S.R.

    1990-01-01

    Our original application aimed to identify genes outside the common nod region involved in nodulation and host range of alfalfa. This has been revised by adding other studies on nodulation gene action and removing molecular studies of gene action. Our restated goals and progress are as follows. An early goal was identification and characterization of additional nodulation genes. By means of transposon mutagenesis, mapping and marker exchange we have established 87 independent mutations in a 20kb area represented by plasmid pRmJT5. We discovered four new genes: nodP, nodD3, syrA and syrM. The sequence, start site and protein product for nodFe, nodG, and nodH were also identified. Regulation of nod FEGH was studied. nod FEGH can be induced by luteolin in the presence of noodle; nodD1; noD3 and syrM, a symbiotic regulator gene also increase transcription of nod FEGH. syrA will interact with syrM; syrM also regulates exopolysaccharide genes and is believed to be a master regulator. As part of these studies, an in vitro transcription/translation system for Rhizobium was developed. Adjacent to nodP we discussed nodQ, nodPQ occurrs in two highly consumed copies. nodQ appears by sequence analysis to be similar to initiation and elongation factors, with the highest homology in the GDP binding domain. We have also investigated the nod strain, WL131. WL131 has an insertion, ISRm3, interrupting nodG, and a nonsase mutation in nodH, nodH is responsible for the lack of nodulation. We are currently investigating supernatant factors, host range effects C by spot inoculation, glucaronidase fusion proteins, and are developing, a single root hair inoculation protocol. 7 refs., 6 figs., 1 tab.

  10. A Medicago truncatula Cystathionine-β-Synthase-like Domain-Containing Protein Is Required for Rhizobial Infection and Symbiotic Nitrogen Fixation1[OPEN

    PubMed Central

    Breakspear, Andrew; Guan, Dian; Nakashima, Jin; Zhang, Shulan; Torres-Jerez, Ivone; Oldroyd, Giles; Murray, Jeremy D.; Udvardi, Michael K.

    2016-01-01

    The symbiosis between leguminous plants and soil rhizobia culminates in the formation of nitrogen-fixing organs called nodules that support plant growth. Two Medicago truncatula Tnt1-insertion mutants were identified that produced small nodules, which were unable to fix nitrogen effectively due to ineffective rhizobial colonization. The gene underlying this phenotype was found to encode a protein containing a putative membrane-localized domain of unknown function (DUF21) and a cystathionine-β-synthase domain. The cbs1 mutants had defective infection threads that were sometimes devoid of rhizobia and formed small nodules with greatly reduced numbers of symbiosomes. We studied the expression of the gene, designated M. truncatula Cystathionine-β-Synthase-like1 (MtCBS1), using a promoter-β-glucuronidase gene fusion, which revealed expression in infected root hair cells, developing nodules, and in the invasion zone of mature nodules. An MtCBS1-GFP fusion protein localized itself to the infection thread and symbiosomes. Nodulation factor-induced Ca2+ responses were observed in the cbs1 mutant, indicating that MtCBS1 acts downstream of nodulation factor signaling. MtCBS1 expression occurred exclusively during Medicago-rhizobium symbiosis. Induction of MtCBS1 expression during symbiosis was found to be dependent on Nodule Inception (NIN), a key transcription factor that controls both rhizobial infection and nodule organogenesis. Interestingly, the closest homolog of MtCBS1, MtCBS2, was specifically induced in mycorrhizal roots, suggesting common infection mechanisms in nodulation and mycorrhization. Related proteins in Arabidopsis have been implicated in cell wall maturation, suggesting a potential role for CBS1 in the formation of the infection thread wall. PMID:26884486

  11. A Medicago truncatula Cystathionine-β-Synthase-like Domain-Containing Protein Is Required for Rhizobial Infection and Symbiotic Nitrogen Fixation.

    PubMed

    Sinharoy, Senjuti; Liu, Chengwu; Breakspear, Andrew; Guan, Dian; Shailes, Sarah; Nakashima, Jin; Zhang, Shulan; Wen, Jiangqi; Torres-Jerez, Ivone; Oldroyd, Giles; Murray, Jeremy D; Udvardi, Michael K

    2016-04-01

    The symbiosis between leguminous plants and soil rhizobia culminates in the formation of nitrogen-fixing organs called nodules that support plant growth. Two Medicago truncatula Tnt1-insertion mutants were identified that produced small nodules, which were unable to fix nitrogen effectively due to ineffective rhizobial colonization. The gene underlying this phenotype was found to encode a protein containing a putative membrane-localized domain of unknown function (DUF21) and a cystathionine-β-synthase domain. The cbs1 mutants had defective infection threads that were sometimes devoid of rhizobia and formed small nodules with greatly reduced numbers of symbiosomes. We studied the expression of the gene, designated M truncatula Cystathionine-β-Synthase-like1 (MtCBS1), using a promoter-β-glucuronidase gene fusion, which revealed expression in infected root hair cells, developing nodules, and in the invasion zone of mature nodules. An MtCBS1-GFP fusion protein localized itself to the infection thread and symbiosomes. Nodulation factor-induced Ca(2+) responses were observed in the cbs1 mutant, indicating that MtCBS1 acts downstream of nodulation factor signaling. MtCBS1 expression occurred exclusively during Medicago-rhizobium symbiosis. Induction of MtCBS1 expression during symbiosis was found to be dependent on Nodule Inception (NIN), a key transcription factor that controls both rhizobial infection and nodule organogenesis. Interestingly, the closest homolog of MtCBS1, MtCBS2, was specifically induced in mycorrhizal roots, suggesting common infection mechanisms in nodulation and mycorrhization. Related proteins in Arabidopsis have been implicated in cell wall maturation, suggesting a potential role for CBS1 in the formation of the infection thread wall. PMID:26884486

  12. [Factors of multiple resistance to antibiotics in nodule bacteria].

    PubMed

    Pariĭskaia, A N; Gorelova, O P

    1976-01-01

    Multiple resistance to antibiotics (penicillin, levomycetin, neomycin, tetracycline) was found in 15% of collection strains of nodule bacteria and in strains isolated from natural environment. PMID:1050635

  13. Nodulation outer proteins: double-edged swords of symbiotic rhizobia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizobia are nitrogen-fixing bacteria that establish a nodule symbiosis with legumes. Nodule formation is the result of a complex bacterial infection process, which depends on signals and surface determinants produced by both symbiotic partners. Among them, rhizobial nodulation outer proteins (Nops)...

  14. The root hair "infectome" of Medicago truncatula uncovers changes in cell cycle genes and reveals a requirement for Auxin signaling in rhizobial infection.

    PubMed

    Breakspear, Andrew; Liu, Chengwu; Roy, Sonali; Stacey, Nicola; Rogers, Christian; Trick, Martin; Morieri, Giulia; Mysore, Kirankumar S; Wen, Jiangqi; Oldroyd, Giles E D; Downie, J Allan; Murray, Jeremy D

    2014-12-01

    Nitrogen-fixing rhizobia colonize legume roots via plant-made intracellular infection threads. Genetics has identified some genes involved but has not provided sufficient detail to understand requirements for infection thread development. Therefore, we transcriptionally profiled Medicago truncatula root hairs prior to and during the initial stages of infection. This revealed changes in the responses to plant hormones, most notably auxin, strigolactone, gibberellic acid, and brassinosteroids. Several auxin responsive genes, including the ortholog of Arabidopsis thaliana Auxin Response Factor 16, were induced at infection sites and in nodule primordia, and mutation of ARF16a reduced rhizobial infection. Associated with the induction of auxin signaling genes, there was increased expression of cell cycle genes including an A-type cyclin and a subunit of the anaphase promoting complex. There was also induction of several chalcone O-methyltransferases involved in the synthesis of an inducer of Sinorhizobium meliloti nod genes, as well as a gene associated with Nod factor degradation, suggesting both positive and negative feedback loops that control Nod factor levels during rhizobial infection. We conclude that the onset of infection is associated with reactivation of the cell cycle as well as increased expression of genes required for hormone and flavonoid biosynthesis and that the regulation of auxin signaling is necessary for initiation of rhizobial infection threads. PMID:25527707

  15. Rhizobial peptidase HrrP cleaves host-encoded signaling peptides and mediates symbiotic compatibility

    PubMed Central

    Price, Paul A.; Tanner, Houston R.; Dillon, Brett A.; Shabab, Mohammed; Walker, Graham C.; Griffitts, Joel S.

    2015-01-01

    Legume–rhizobium pairs are often observed that produce symbiotic root nodules but fail to fix nitrogen. Using the Sinorhizobium meliloti and Medicago truncatula symbiotic system, we previously described several naturally occurring accessory plasmids capable of disrupting the late stages of nodule development while enhancing bacterial proliferation within the nodule. We report here that host range restriction peptidase (hrrP), a gene found on one of these plasmids, is capable of conferring both these properties. hrrP encodes an M16A family metallopeptidase whose catalytic activity is required for these symbiotic effects. The ability of hrrP to suppress nitrogen fixation is conditioned upon the genotypes of both the host plant and the hrrP-expressing rhizobial strain, suggesting its involvement in symbiotic communication. Purified HrrP protein is capable of degrading a range of nodule-specific cysteine-rich (NCR) peptides encoded by M. truncatula. NCR peptides are crucial signals used by M. truncatula for inducing and maintaining rhizobial differentiation within nodules, as demonstrated in the accompanying article [Horváth B, et al. (2015) Proc Natl Acad Sci USA, 10.1073/pnas.1500777112]. The expression pattern of hrrP and its effects on rhizobial morphology are consistent with the NCR peptide cleavage model. This work points to a symbiotic dialogue involving a complex ensemble of host-derived signaling peptides and bacterial modifier enzymes capable of adjusting signal strength, sometimes with exploitative outcomes. PMID:26401024

  16. Alfalfa Enod12 genes are differentially regulated during nodule development by Nod factors and Rhizobium invasion.

    PubMed Central

    Bauer, P; Crespi, M D; Szécsi, J; Allison, L A; Schultze, M; Ratet, P; Kondorosi, E; Kondorosi, A

    1994-01-01

    MsEnod12A and MsEnod12B are two early nodulin genes from alfalfa (Medicago sativa). Differential expression of these genes was demonstrated using a reverse transcription-polymerase chain reaction approach. MsEnod12A RNA was detected only in nodules and not in other plant tissues. In contrast, MsEnod12B transcripts were found in nodules and also at low levels in roots, flowers, stems, and leaves. MsEnod12B expression was enhanced in the root early after inoculation with the microsymbiont Rhizobium meliloti and after treatment with purified Nod factors, whereas MsEnod12A induction was detected only when developing nodules were visible. In situ hybridization showed that in nodules, MsEnod12 expression occurred in the infection zone. In empty Fix- nodules the MsEnod12A transcript level was much reduced, and in spontaneous nodules it was not detectable. These data indicate that MsEnod12B expression in roots is related to the action of Nod factors, whereas MsEnod12A expression is associated with the invasion process in nodules. Therefore, alfalfa possesses different mechanisms regulating MsEnod12A and MsEnod12B expression. PMID:8066132

  17. EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation in Medicago truncatula[W

    PubMed Central

    Vernié, Tatiana; Moreau, Sandra; de Billy, Françoise; Plet, Julie; Combier, Jean-Philippe; Rogers, Christian; Oldroyd, Giles; Frugier, Florian; Niebel, Andreas; Gamas, Pascal

    2008-01-01

    Mechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. Here, we describe EFD (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in Medicago truncatula. The EFD transcription factor belongs to the ethylene response factor (ERF) group V, which contains ERN1, 2, and 3, three ERFs involved in Nod factor signaling. The role of EFD in the regulation of nodulation was examined through the characterization of a null deletion mutant (efd-1), RNA interference, and overexpression studies. These studies revealed that EFD is a negative regulator of root nodulation and infection by Rhizobium and that EFD is required for the formation of functional nitrogen-fixing nodules. EFD appears to be involved in the plant and bacteroid differentiation processes taking place beneath the nodule meristem. We also showed that EFD activated Mt RR4, a cytokinin primary response gene that encodes a type-A response regulator. We propose that EFD induction of Mt RR4 leads to the inhibition of cytokinin signaling, with two consequences: the suppression of new nodule initiation and the activation of differentiation as cells leave the nodule meristem. Our work thus reveals a key regulator linking early and late stages of nodulation and suggests that the regulation of the cytokinin pathway is important both for nodule initiation and development. PMID:18978033

  18. DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways.

    PubMed

    Jin, Yue; Liu, Huan; Luo, Dexian; Yu, Nan; Dong, Wentao; Wang, Chao; Zhang, Xiaowei; Dai, Huiling; Yang, Jun; Wang, Ertao

    2016-01-01

    Legumes form symbiotic associations with either nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. Formation of these two symbioses is regulated by a common set of signalling components that act downstream of recognition of rhizobia or mycorrhizae by host plants. Central to these pathways is the calcium and calmodulin-dependent protein kinase (CCaMK)-IPD3 complex which initiates nodule organogenesis following calcium oscillations in the host nucleus. However, downstream signalling events are not fully understood. Here we show that Medicago truncatula DELLA proteins, which are the central regulators of gibberellic acid signalling, positively regulate rhizobial symbiosis. Rhizobia colonization is impaired in della mutants and we provide evidence that DELLAs can promote CCaMK-IPD3 complex formation and increase the phosphorylation state of IPD3. DELLAs can also interact with NSP2-NSP1 and enhance the expression of Nod-factor-inducible genes in protoplasts. We show that DELLA is able to bridge a protein complex containing IPD3 and NSP2. Our results suggest a transcriptional framework for regulation of root nodule symbiosis. PMID:27514472

  19. DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways

    PubMed Central

    Jin, Yue; Liu, Huan; Luo, Dexian; Yu, Nan; Dong, Wentao; Wang, Chao; Zhang, Xiaowei; Dai, Huiling; Yang, Jun; Wang, Ertao

    2016-01-01

    Legumes form symbiotic associations with either nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. Formation of these two symbioses is regulated by a common set of signalling components that act downstream of recognition of rhizobia or mycorrhizae by host plants. Central to these pathways is the calcium and calmodulin-dependent protein kinase (CCaMK)–IPD3 complex which initiates nodule organogenesis following calcium oscillations in the host nucleus. However, downstream signalling events are not fully understood. Here we show that Medicago truncatula DELLA proteins, which are the central regulators of gibberellic acid signalling, positively regulate rhizobial symbiosis. Rhizobia colonization is impaired in della mutants and we provide evidence that DELLAs can promote CCaMK–IPD3 complex formation and increase the phosphorylation state of IPD3. DELLAs can also interact with NSP2–NSP1 and enhance the expression of Nod-factor-inducible genes in protoplasts. We show that DELLA is able to bridge a protein complex containing IPD3 and NSP2. Our results suggest a transcriptional framework for regulation of root nodule symbiosis. PMID:27514472

  20. How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model

    PubMed Central

    Jones, Kathryn M.; Kobayashi, Hajime; Davies, Bryan W.; Taga, Michiko E.; Walker, Graham C.

    2009-01-01

    Nitrogen-fixing rhizobial bacteria and leguminous plants have evolved complex signal exchange mechanisms that allow a specific bacterial species to induce its host plant to form invasion structures through which the bacteria can enter the plant root. Once the bacteria have been endocytosed within a host-membrane-bound compartment by root cells, the bacteria differentiate into a new form that can convert atmospheric nitrogen into ammonia. Bacterial differentiation and nitrogen fixation are dependent on the microaerobic environment and other support factors provided by the plant. In return, the plant receives nitrogen from the bacteria, which allows it to grow in the absence of an external nitrogen source. Here, we review recent discoveries about the mutual recognition process that allows the model rhizobial symbiont Sinorhizobium meliloti to invade and differentiate inside its host plant alfalfa (Medicago sativa) and the model host plant barrel medic (Medicago truncatula). PMID:17632573

  1. KNOTTED1-LIKE HOMEOBOX 3: a new regulator of symbiotic nodule development

    PubMed Central

    Azarakhsh, M.; Kirienko, A. N.; Zhukov, V. A.; Lebedeva, M. A.; Dolgikh, E. A.; Lutova, L. A.

    2015-01-01

    KNOX transcription factors (TFs) regulate different aspects of plant development essentially through their effects on phytohormone metabolism. In particular, KNOX TF SHOOTMERISTEMLESS activates the cytokinin biosynthesis ISOPENTENYL TRANSFERASE (IPT) genes in the shoot apical meristem. However, the role of KNOX TFs in symbiotic nodule development and their possible effects on phytohormone metabolism during nodulation have not been studied to date. Cytokinin is a well-known regulator of nodule development, playing the key role in the regulation of cell division during nodule primordium formation. Recently, the activation of IPT genes was shown to take place during nodulation. Therefore, it was hypothesized that KNOX TFs may regulate nodule development and activate cytokinin biosynthesis upon nodulation. This study analysed the expression of different KNOX genes in Medicago truncatula Gaertn. and Pisum sativum L. Among them, the KNOX3 gene was upregulated in response to rhizobial inoculation in both species. pKNOX3::GUS activity was observed in developing nodule primordium. KNOX3 ectopic expression caused the formation of nodule-like structures on transgenic root without bacterial inoculation, a phenotype similar to one described previously for legumes with constitutive activation of the cytokinin receptor. Furthermore, in transgenic roots with MtKNOX3 knockdown, downregulation of A-type cytokinin response genes was found, as well as the MtIPT3 and LONELYGUY2 (MtLOG2) gene being involved in cytokinin activation. Taken together, these findings suggest that KNOX3 gene is involved in symbiotic nodule development and may regulate cytokinin biosynthesis/activation upon nodule development in legume plants. PMID:26351356

  2. KNOTTED1-LIKE HOMEOBOX 3: a new regulator of symbiotic nodule development.

    PubMed

    Azarakhsh, M; Kirienko, A N; Zhukov, V A; Lebedeva, M A; Dolgikh, E A; Lutova, L A

    2015-12-01

    KNOX transcription factors (TFs) regulate different aspects of plant development essentially through their effects on phytohormone metabolism. In particular, KNOX TF SHOOTMERISTEMLESS activates the cytokinin biosynthesis ISOPENTENYL TRANSFERASE (IPT) genes in the shoot apical meristem. However, the role of KNOX TFs in symbiotic nodule development and their possible effects on phytohormone metabolism during nodulation have not been studied to date. Cytokinin is a well-known regulator of nodule development, playing the key role in the regulation of cell division during nodule primordium formation. Recently, the activation of IPT genes was shown to take place during nodulation. Therefore, it was hypothesized that KNOX TFs may regulate nodule development and activate cytokinin biosynthesis upon nodulation. This study analysed the expression of different KNOX genes in Medicago truncatula Gaertn. and Pisum sativum L. Among them, the KNOX3 gene was upregulated in response to rhizobial inoculation in both species. pKNOX3::GUS activity was observed in developing nodule primordium. KNOX3 ectopic expression caused the formation of nodule-like structures on transgenic root without bacterial inoculation, a phenotype similar to one described previously for legumes with constitutive activation of the cytokinin receptor. Furthermore, in transgenic roots with MtKNOX3 knockdown, downregulation of A-type cytokinin response genes was found, as well as the MtIPT3 and LONELYGUY2 (MtLOG2) gene being involved in cytokinin activation. Taken together, these findings suggest that KNOX3 gene is involved in symbiotic nodule development and may regulate cytokinin biosynthesis/activation upon nodule development in legume plants. PMID:26351356

  3. Is occupationally induced exposure to radiation a risk factor for thyroid nodule formation?

    SciTech Connect

    Antonelli, A.; Silvano, G.; Gambuzza, C.; Bianchi, F.; Tana, L.; Baschieri, L.

    1996-05-01

    The prevalance of thyroid nodules was studied with ultrasonography in a group of male hospital workers (n = 44) who had been exposed occupationally to x-rays. This group was compared with a group of nonexposed workers (n = 88) who were age- and sex-matched with the exposed workers. Thyroid nodules were detected in 18 (41%) of the exposed workers, compared with 11 (13%) of the nonexposed controls. Both groups were subdivided with respect to age (i.e., 30-39 y, 40-49 y, 50-59 y), and there was a higher and significant relative risk for thyroid nodule formation in the exposed group. We also divided the groups into subgroups according to levels of exposure (i.e., nonexposed, exposed for {le} 20 y, and exposed for {ge} 20 y), and a significant result was obtained with the linear-trend chi-square test. The preliminary results of our study suggest that occupationally induced exposure to radiation may be a risk factor for thyroid nodule formation. 9 refs., 2 tabs.

  4. Prognostic Factors in Terms of the Number of Metastatic Nodules in Patients With Colorectal Cancer Liver Metastases

    PubMed Central

    Jang, Ki Ung; Kim, Chan Wook; Kim, Ki-Hun; Lim, Seok-Byung; Yu, Chang Sik; Kim, Tae Won; Kim, Pyo Nyun; Kim, Jong Hoon

    2016-01-01

    Purpose The hepatic resection is the gold-standard treatment for patients with colorectal-cancer liver metastases (CLM). This study aimed to identify prognostic factors in patients with synchronous CLM who underwent a surgical curative (R0) resection with respect to the number of metastatic nodules. Methods Of 1,261 CLM patients treated between January 1991 and December 2010, 339 who underwent a R0 resection for synchronous CLM were included in this retrospective analysis. Patients were grouped according to the number of CLM nodules: 1–2 CLM nodules, n = 272 (group 1) and 3–8 CLM nodules, n = 67 (group 2). Results The 5-year progression-free survival (PFS) rate in group 1was better than that in group 2 (P = 0.020). The multivariate analysis identified lymph-node metastasis (N2), lymphovascular invasion (LVI), and three or more CLM nodules as independent poor prognostic factors for PFS in all patients and lymph-node metastasis (N2) and LVI as independent poor prognostic factors for patients in group 1. No independent prognostic factors were identified for patients in group 2. CLM treatment method and neoadjuvant chemotherapy were not associated with survival. Conclusion Three or more metastatic nodules, lymph-node metastasis (N2), and LVI were independent poor prognostic factors for PFS in patients with synchronous CLM who underwent a R0 resection. The latter 2 factors were also independent prognostic factors for PFS in patients with less than 3 CLM nodules; however, in patients with three or more CLM nodules, the prognosis for PFS may be related only to liver metastasis. PMID:27437390

  5. Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine.

    PubMed

    Yan, Hui; Yan, Jun; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin; Zhang, Xiao Xia; Chen, Wen Feng

    2016-09-01

    Rhizobial strains from root nodules of Astragalus mongholicus and soybean (Glycine max) were characterized phylogenetically as members of the genus Ensifer (formerly named Sinorhizobium), based on 16S rRNA gene sequence comparisons. Results based upon concatenated sequence analysis of three housekeeping genes (recA, atpD and glnII, ≤ 93.8 % similarities to known species) and average nucleotide identity (ANI) values of whole genome sequence comparisons (ranging from 89.6 % to 83.4 % to Ensifer fredii and Ensifer saheli, respectively) indicated the distinct positions of these novel strains within the genus Ensifer. Phylogeny of symbiotic genes (nodC and nifH) of three novel strains clustered them with rhizobial species Ensifer fredii and Ensifer sojae, both isolated from nodules of Glycine max. Cross-nodulation tests showed that the representative strain CCBAU 23380T could form root nodules with nitrogen fixation capability on Glycine soja, Albizia julibrissin, Vigna unguiculata and Cajanus cajan, but failed to nodulate Astragalus mongholicus, its original host legume. Strain CCBAU 23380T formed inefficient nodules on G. max, and it did not contain 18 : 0, 18 : 1ω7c 11-methyl or summed feature 1 fatty acids, which differed from other related strains. Failure to utilize malonic acid as a carbon source distinguished strain CCBAU 23380T from the type strains of related species. The genome size of CCBAU 23380T was 6.0 Mbp, comprising 5624 predicted genes with DNA G+C content of 62.4 mol%. Based on the results above, a novel species, Ensifer glycinis sp. nov., is proposed, with CCBAU 23380T (=LMG 29231T =HAMBI 3645T) as the type strain. PMID:27125987

  6. Atypical Rheumatoid Nodules: A Possible Precursor to a Rheumatoid Variant in a Rheumatoid-Factor-Negative Patient. Case Report

    PubMed Central

    Kim, Sharon; Parker, Wendy L.

    2008-01-01

    Subcutaneous nodules occur in approximately 20–25% of rheumatoid factor (RF)-positive rheumatoid patients. In this paper, we present a unique case of a 47-year-old healthy RF-negative woman with a 3-year history of necrobiotic nodules over the dorsum of her hands, extensor forearms, and lower extremities. This may represent an atypical presentation or a new rheumatoid variant. PMID:19048351

  7. Bradyrhizobium sp. Strains That Nodulate the Leguminous Tree Acacia albida Produce Fucosylated and Partially Sulfated Nod Factors

    PubMed Central

    Ferro, Myriam; Lorquin, Jean; Ba, Salif; Sanon, Kadidia; Promé, Jean-Claude; Boivin, Catherine

    2000-01-01

    We determined the structures of Nod factors produced by six different Bradyrhizobium sp. strains nodulating the legume tree Acacia albida (syn. Faidherbia albida). Compounds from all strains were found to be similar, i.e., O-carbamoylated and substituted by an often sulfated methyl fucose and different from compounds produced by Rhizobium-Mesorhizobium-Sinorhizobium strains nodulating other species of the Acaciae tribe. PMID:11055966

  8. Diversity of field isolates of sinorhizobium meliloti nodulating alfalfa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most alfalfa seed is treated with a rhizobial inoculant consisting of one or more strains of Sinorhizobium meliloti before planting to enhance nodulation of seedlings. However, little is known about the persistence of inoculated strains later in the season. There is also a paucity of information on ...

  9. Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis.

    PubMed Central

    Laguerre, G; van Berkum, P; Amarger, N; Prévost, D

    1997-01-01

    The genetic diversity of 44 rhizobial isolates from Astragalus, Oxytropis, and Onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (MRSP) analysis of 16S rRNA genes and by PCR DNA fingerprinting with repetitive sequences (REP-PCR). A comparison of tree topologies of reference strains constructed with data obtained by MRSP and by 16S rRNA gene sequence analyses showed that the topologies were in good agreement, indicating that the MSRP approach results in reasonable estimates of rhizobial phylogeny. The isolates were distributed into 14 distinct 16S rRNA gene types clustering into three major groups which corresponded with three of the genera within the legume symbionts. Most of the isolates were within the genus Mesorhizobium. Five were identified with different genomic species nodulating Lotus spp. and Cicer arietinum. Three Astragalus isolates were classified as Bradyrhizobium, one being similar to Bradyrhizobium elkanii and another being similar to Bradyrhizobium japonicum. Six of the isolates were related to species within the genus Rhizobium. Two were similar to Rhizobium leguminosarum, and the remainder were identified as Rhizobium gallicum. DNA fingerprinting by REP-PCR revealed a high level of diversity within single 16S ribosomal DNA types. The 44 isolates were distributed into 34 REP groups. Rhizobial classification at the genus and probably also the species levels was independent of geographic origin and host plant affinity. PMID:9406393

  10. Effects of transforming growth factor beta and epidermal growth factor on cell proliferation and the formation of bone nodules in isolated fetal rat calvaria cells.

    PubMed

    Antosz, M E; Bellows, C G; Aubin, J E

    1989-08-01

    When cells enzymatically isolated from fetal rat calvaria (RC cells) are cultured in vitro in the presence of ascorbic acid and Na beta-glycerophosphate, discrete three-dimensional nodules form with the histologic, immunohistochemical, and ultrastructural characteristics of bone (Bellows et al; Calcified Tissue International 38:143-154, 1986; Bhargava et al., Bone, 9:155-163, 1988). Quantitation of the number of bone nodules that forms provides a colony assay for osteoprogenitor cells present in the RC population (Bellows and Aubin, Develop. Biol., 133:8-13, 1989). Continuous culture with either epidermal growth factor (EGF) or transforming growth factor beta (TGF-beta) results in dose-dependent inhibition of bone nodule formation; however, the former causes increased proliferation and saturation density, while the latter reduces both parameters. Addition of EGF (48 h pulse, 2-200 ng/ml) to RC cells at day 1 after plating results in increased proliferation and population saturation density and an increased number of bone nodules formed. Similar pulses at confluence and in postconfluent multilayered cultures when nodules first begin forming (approx. day 11) inhibited bone nodule formation and resulted in a smaller stimulation of cell proliferation. Forty-eight hour pulses of TGF-beta (0.01-1 ng/ml) reduced bone nodule formation and proliferation at all times examined, with pulses on day 1 causing maximum inhibition. The effects of pulses with TGF-beta and EGF on inhibition of nodule formation are independent of the presence of serum in the culture medium during the pulse. The data suggest that whereas EGF can either stimulate or inhibit the formation of bone nodules depending upon the time and duration of exposure, TGF-B inhibits bone nodule formation under all conditions tested. Moreover, these effects on osteoprogenitor cell differentiation do not always correlate with the effects of the growth factors on RC cell proliferation. PMID:2787326

  11. Soybean miR172c Targets the Repressive AP2 Transcription Factor NNC1 to Activate ENOD40 Expression and Regulate Nodule Initiation[C][W

    PubMed Central

    Wang, Youning; Wang, Lixiang; Zou, Yanmin; Chen, Liang; Cai, Zhaoming; Zhang, Senlei; Zhao, Fang; Tian, Yinping; Jiang, Qiong; Ferguson, Brett J.; Gresshoff, Peter M.; Li, Xia

    2014-01-01

    MicroRNAs are noncoding RNAs that act as master regulators to modulate various biological processes by posttranscriptionally repressing their target genes. Repression of their target mRNA(s) can modulate signaling cascades and subsequent cellular events. Recently, a role for miR172 in soybean (Glycine max) nodulation has been described; however, the molecular mechanism through which miR172 acts to regulate nodulation has yet to be explored. Here, we demonstrate that soybean miR172c modulates both rhizobium infection and nodule organogenesis. miR172c was induced in soybean roots inoculated with either compatible Bradyrhizobium japonicum or lipooligosaccharide Nod factor and was highly upregulated during nodule development. Reduced activity and overexpression of miR172c caused dramatic changes in nodule initiation and nodule number. We show that soybean miR172c regulates nodule formation by repressing its target gene, Nodule Number Control1, which encodes a protein that directly targets the promoter of the early nodulin gene, ENOD40. Interestingly, transcriptional levels of miR172c were regulated by both Nod Factor Receptor1α/5α-mediated activation and by autoregulation of nodulation-mediated inhibition. Thus, we established a direct link between miR172c and the Nod factor signaling pathway in addition to adding a new layer to the precise nodulation regulation mechanism of soybean. PMID:25549672

  12. The NIN Transcription Factor Coordinates Diverse Nodulation Programs in Different Tissues of the Medicago truncatula Root[OPEN

    PubMed Central

    Kim, Jiyoung; Frances, Lisa; Ding, Yiliang; Sun, Jongho; Guan, Dian; de Carvalho-Niebel, Fernanda; Oldroyd, Giles E.D.

    2015-01-01

    Biological nitrogen fixation in legumes occurs in nodules that are initiated in the root cortex following Nod factor recognition at the root surface, and this requires coordination of diverse developmental programs in these different tissues. We show that while early Nod factor signaling associated with calcium oscillations is limited to the root surface, the resultant activation of Nodule Inception (NIN) in the root epidermis is sufficient to promote cytokinin signaling and nodule organogenesis in the inner root cortex. NIN or a product of its action must be associated with the transmission of a signal between the root surface and the cortical cells where nodule organogenesis is initiated. NIN appears to have distinct functions in the root epidermis and the root cortex. In the epidermis, NIN restricts the extent of Early Nodulin 11 (ENOD11) expression and does so through competitive inhibition of ERF Required for Nodulation (ERN1). In contrast, NIN is sufficient to promote the expression of the cytokinin receptor Cytokinin Response 1 (CRE1), which is restricted to the root cortex. Our work in Medicago truncatula highlights the complexity of NIN action and places NIN as a central player in the coordination of the symbiotic developmental programs occurring in differing tissues of the root that combined are necessary for a nitrogen-fixing symbiosis. PMID:26672071

  13. NrcR, a New Transcriptional Regulator of Rhizobium tropici CIAT 899 Involved in the Legume Root-Nodule Symbiosis

    PubMed Central

    del Cerro, Pablo; Rolla-Santos, Amanda A. P.; Valderrama-Fernández, Rocío; Gil-Serrano, Antonio; Bellogín, Ramón A.; Gomes, Douglas Fabiano; Pérez-Montaño, Francisco; Megías, Manuel; Hungría, Mariangela; Ollero, Francisco Javier

    2016-01-01

    The establishment of nitrogen-fixing rhizobium-legume symbioses requires a highly complex cascade of events. In this molecular dialogue the bacterial NodD transcriptional regulators in conjunction with plant inducers, mostly flavonoids, are responsible for the biosynthesis and secretion of Nod factors which are key molecules for successful nodulation. Other transcriptional regulators related to the symbiotic process have been identified in rhizobial genomes, including negative regulators such as NolR. Rhizobium tropici CIAT 899 is an important symbiont of common bean (Phaseolus vulgaris L.), and its genome encompasses intriguing features such as five copies of nodD genes, as well as other possible transcriptional regulators including the NolR protein. Here we describe and characterize a new regulatory gene located in the non-symbiotic plasmid pRtrCIAT899c, that shows homology (46% identity) with the nolR gene located in the chromosome of CIAT 899. The mutation of this gene, named nrcR (nolR-like plasmid c Regulator), enhanced motility and exopolysaccharide production in comparison to the wild-type strain. Interestingly, the number and decoration of Nod Factors produced by this mutant were higher than those detected in the wild-type strain, especially under salinity stress. The nrcR mutant showed delayed nodulation and reduced competitiveness with P. vulgaris, and reduction in nodule number and shoot dry weight in both P. vulgaris and Leucaena leucocephala. Moreover, the mutant exhibited reduced capacity to induce the nodC gene in comparison to the wild-type CIAT 899. The finding of a new nod-gene regulator located in a non-symbiotic plasmid may reveal the existence of even more complex mechanisms of regulation of nodulation genes in R. tropici CIAT 899 that may be applicable to other rhizobial species. PMID:27096734

  14. NrcR, a New Transcriptional Regulator of Rhizobium tropici CIAT 899 Involved in the Legume Root-Nodule Symbiosis.

    PubMed

    Del Cerro, Pablo; Rolla-Santos, Amanda A P; Valderrama-Fernández, Rocío; Gil-Serrano, Antonio; Bellogín, Ramón A; Gomes, Douglas Fabiano; Pérez-Montaño, Francisco; Megías, Manuel; Hungría, Mariangela; Ollero, Francisco Javier

    2016-01-01

    The establishment of nitrogen-fixing rhizobium-legume symbioses requires a highly complex cascade of events. In this molecular dialogue the bacterial NodD transcriptional regulators in conjunction with plant inducers, mostly flavonoids, are responsible for the biosynthesis and secretion of Nod factors which are key molecules for successful nodulation. Other transcriptional regulators related to the symbiotic process have been identified in rhizobial genomes, including negative regulators such as NolR. Rhizobium tropici CIAT 899 is an important symbiont of common bean (Phaseolus vulgaris L.), and its genome encompasses intriguing features such as five copies of nodD genes, as well as other possible transcriptional regulators including the NolR protein. Here we describe and characterize a new regulatory gene located in the non-symbiotic plasmid pRtrCIAT899c, that shows homology (46% identity) with the nolR gene located in the chromosome of CIAT 899. The mutation of this gene, named nrcR (nolR-like plasmid c Regulator), enhanced motility and exopolysaccharide production in comparison to the wild-type strain. Interestingly, the number and decoration of Nod Factors produced by this mutant were higher than those detected in the wild-type strain, especially under salinity stress. The nrcR mutant showed delayed nodulation and reduced competitiveness with P. vulgaris, and reduction in nodule number and shoot dry weight in both P. vulgaris and Leucaena leucocephala. Moreover, the mutant exhibited reduced capacity to induce the nodC gene in comparison to the wild-type CIAT 899. The finding of a new nod-gene regulator located in a non-symbiotic plasmid may reveal the existence of even more complex mechanisms of regulation of nodulation genes in R. tropici CIAT 899 that may be applicable to other rhizobial species. PMID:27096734

  15. Root Hair Deformation Activity of Nodulation Factors and Their Fate on Vicia sativa.

    PubMed Central

    Heidstra, R.; Geurts, R.; Franssen, H.; Spaink, H. P.; Van Kammen, A.; Bisseling, T.

    1994-01-01

    We used a semiquantitative root hair deformation assay for Vicia sativa (vetch) to study the activity of Rhizobium leguminosarum bv viciae nodulation (Nod) factors. Five to 10 min of Nod factor-root interaction appears to be sufficient to induce root hair deformation. The first deformation is visible within 1 h, and after 3 h about 80% of the root hairs in a small susceptible zone of the root are deformed. This zone encompasses root hairs that have almost reached their maximal size. The Nod factor accumulates preferentially to epidermal cells of the young part of the root, but is not restricted to the susceptible zone. In the interaction with roots, the glucosamine backbone of Nod factors is shortened, presumably by chitinases. NodRlv-IV(C18:4,Ac) is more stable than NodRlv-V(C18:4,Ac). No correlation was found between Nod factor degradation and susceptibility. Degradation occurs both in the susceptible zone and in the mature zone. Moreover, degradation is not affected by NH4NO3 and is similar in vetch and in the nonhost alfalfa (Medicago sativa). PMID:12232242

  16. Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes.

    PubMed

    Granqvist, Emma; Sun, Jongho; Op den Camp, Rik; Pujic, Petar; Hill, Lionel; Normand, Philippe; Morris, Richard J; Downie, J Allan; Geurts, Rene; Oldroyd, Giles E D

    2015-08-01

    Plants that form root-nodule symbioses are within a monophyletic 'nitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca(2+) ), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal. In this study we expanded the species analysed for activation of Ca(2+) oscillations, including nonleguminous species within the nitrogen-fixing clade. We showed that Ca(2+) oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca(2+) oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca(2+) oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors. We conclude that the ability to mount Ca(2+) oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade. PMID:26010117

  17. The Role of Flavonoids in Nodulation Host-Range Specificity: An Update.

    PubMed

    Liu, Cheng-Wu; Murray, Jeremy D

    2016-01-01

    Flavonoids are crucial signaling molecules in the symbiosis between legumes and their nitrogen-fixing symbionts, the rhizobia. The primary function of flavonoids in the interaction is to induce transcription of the genes for biosynthesis of the rhizobial signaling molecules called Nod factors, which are perceived by the plant to allow symbiotic infection of the root. Many legumes produce specific flavonoids that only induce Nod factor production in homologous rhizobia, and therefore act as important determinants of host range. Despite a wealth of evidence on legume flavonoids, relatively few have proven roles in rhizobial infection. Recent studies suggest that production of key "infection" flavonoids is highly localized at infection sites. Furthermore, some of the flavonoids being produced at infection sites are phytoalexins and may have a role in the selection of compatible symbionts during infection. The molecular details of how flavonoid production in plants is regulated during nodulation have not yet been clarified, but nitrogen availability has been shown to play a role. PMID:27529286

  18. An Epidemiological Study of Risk Factors of Thyroid Nodule and Goiter in Chinese Women.

    PubMed

    Zheng, Lei; Yan, Wenhua; Kong, Yue; Liang, Ping; Mu, Yiming

    2015-09-01

    Thyroid nodule (TN) and goiter are two common disorders of the thyroid. Despite their benign nature, both conditions can be associated with multiple pathologic conditions including thyroid cancer. In this study, we conducted a large-scale epidemiological study in Chinese women to identify the risk factors implicated in the occurrence of TN and goiter. We analyzed demographic data, lifestyle, medical history, body height, weight, waist circumference, body mass index (BMI), blood pressure, serum glucose and lipids. In addition, thyroid ultrasonography was performed for all subjects. Our results showed that age, menopause, waist circumference, BMI, hypertension, dyslipidemia, and hyperglycemia were associated with both TN and goiter. Furthermore, we found that the prevalence of TN was significantly affected by the medical management of hypertension. Our study suggests that postmenopausal Chinese women with advanced age, obesity, diabetes, and hypertension have an increased awareness of thyroid examination in the annual physical check. Conversely, patients with TN and goiter of the same population may have a higher incidence of age- and obesity-related metabolic disorders. PMID:26389933

  19. Thyroid nodule

    MedlinePlus

    ... other thyroid blood tests Thyroid ultrasound Thyroid scan (nuclear medicine) Fine needle aspiration biopsy of the nodule or ... Guidelines for Clinical Practice for the Diagnosis and Management of Thyroid Nodules. Endocr Pract. 2010;16(suppl ...

  20. Leguminous plants: inventors of root nodules to accommodate symbiotic bacteria.

    PubMed

    Suzaki, Takuya; Yoro, Emiko; Kawaguchi, Masayoshi

    2015-01-01

    Legumes and a few other plant species can establish a symbiotic relationship with nitrogen-fixing rhizobia, which enables them to survive in a nitrogen-deficient environment. During the course of nodulation, infection with rhizobia induces the dedifferentiation of host cells to form primordia of a symbiotic organ, the nodule, which prepares plants to accommodate rhizobia in host cells. While these nodulation processes are known to be genetically controlled by both plants and rhizobia, recent advances in studies on two model legumes, Lotus japonicus and Medicago truncatula, have provided great insight into the underlying plant-side molecular mechanism. In this chapter, we review such knowledge, with particular emphasis on two key processes of nodulation, nodule development and rhizobial invasion. PMID:25805123

  1. Identification of the rhizobial symbiont of Astragalus glombiformis in Eastern Morocco as Mesorhizobium camelthorni.

    PubMed

    Guerrouj, Kamal; Pérez-Valera, Eduardo; Chahboune, Rajaa; Abdelmoumen, Hanaa; Bedmar, Eulogio J; El Idrissi, Mustapha Missbah

    2013-08-01

    Astragalus gombiformis is a desert symbiotic nitrogen-fixing legume of great nutritional value as fodder for camels and goats. However, there are no data published on the rhizobial bacteria that nodulate this wild legume in northern Africa. Thirty-four rhizobial bacteria were isolated from root nodules of A. gombifomis grown in sandy soils of the South-Eastern of Morocco. Twenty-five isolates were able to renodulate their original host and possessed a nodC gene copy. The phenotypic and genotypic characterizations carried out illustrated the diversity of the isolates. Phenotypic analysis showed that isolates used a great number of carbohydrates as sole carbon source. However, although they were isolated from arid sandy soils, the isolates do not tolerate drought stress applied in vitro. The phenotypic diversity corresponded mainly to the diversity in the use of some carbohydrates. The genetic analysis as assessed by repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) showed that the isolates clustered into 3 groups at a similarity coefficient of 81 %. The nearly-complete 16S rRNA gene sequence from a representative strain of each PCR-group showed they were closely related to members of the genus Mesorhizobium of the family Phyllobactericeae within the Alphaproteobacteria. Sequencing of the housekeeping genes atpD, glnII and recA, and their concatenated phylogenetic analysis, showed they are closely related to Mesorhizobium camelthorni. Sequencing of the symbiotic nodC gene from each strain revealed they had 83.53 % identity with the nodC sequence of the type strain M. camelthorni CCNWXJ 40-4(T.) PMID:23673873

  2. Genetic variability in Bradyrhizobium japonicum strains nodulating soybean [Glycine max (L.) Merrill].

    PubMed

    Torres, Adalgisa Ribeiro; Kaschuk, Glaciela; Saridakis, George P; Hungria, Mariangela

    2012-04-01

    Brazil has succeeded in sustaining production of soybean [Glycine max (L.) Merrill] by relying mainly on symbiotic N(2) fixation, thanks to the selection and use in inoculants of very effective strains of Bradyrhizobium japonicum and Bradyrhizobium elkanii. It is desirable that rhizobial strains used in inoculants have stable genetic and physiological traits, but experience confirms that rhizobial strains nodulating soybean often lose competitiveness in the field. In this study, soybean cultivar BR 16 was single-inoculated with four B. japonicum strains (CIAT 88, CIAT 89, CIAT 104 and CIAT 105) under aseptic conditions. Forty colonies were isolated from nodules produced by each strain. The progenitor strains, the isolates and four other commercially recommended strains were applied separately to the same cultivar under controlled greenhouse conditions. We observed significant variability in nodulation, shoot dry weight, shoot total N, nodule efficiency (total N mass over nodule mass) and BOX-PCR fingerprinting profiles between variant and progenitor strains. Some variant strains resulted in significantly larger responses in terms of shoot total N, dry weight and nodule efficiency, when compared to their progenitor strain. These results highlight the need for intermittent evaluation of stock bacterial cultures to guarantee effective symbiosis after inoculation. Most importantly, it indicates that it is possible to improve symbiotic effectiveness by screening rhizobial strains for higher N(2) fixation capacity within the natural variability that can be found within each progenitor strain. PMID:22805968

  3. The Prevalence of Thyroid Nodules and an Analysis of Related Lifestyle Factors in Beijing Communities.

    PubMed

    Jiang, Hua; Tian, Yongfeng; Yan, Wenhua; Kong, Yue; Wang, Haibin; Wang, Anping; Dou, Jingtao; Liang, Ping; Mu, Yiming

    2016-04-01

    Thyroid nodules (TNs) have annual increasing trends worldwide, and large-scale investigations on the prevalence of TNs in Beijing communities have not been conducted since the introduction of salt iodization in 1995. We performed a cross-sectional study to determine the prevalence of TNs, their epidemiological characteristics, and their correlation with lifestyle factors. A total of 6324 permanent residents aged 18 years or older (mean age, 52.15 ± 11.58 years) from seven representative communities in Beijing were included in the analyses. Once informed consent was obtained, the subjects were asked to complete questionnaires, a physical examination, and thyroid ultrasound. A total of 3100 cases had TNs. The overall prevalence rate was 49.0%, and the age-standardized prevalence was 40.1%, which increased significantly as age increased (p < 0.001). The prevalence was significantly higher in females compared to males (p < 0.001), and it was significantly higher among female current smokers and former smokers compared to non-smokers (p = 0.007). There was no correlation between alcohol consumption and TNs, and there were no significant differences in the prevalence among different groups of taste preference. The prevalence decreased with an increased frequency of seafood intake (p = 0.015) and with higher literacy levels (p < 0.001). The Cochran-Armitage trend test showed that the prevalence significantly increased with decreased physical labor and exercise intensity (p < 0.001, p = 0.009). Logistic regression analysis showed that age (Odds ratio (OR) = 1.039 (1.034-1.044), p < 0.001), the female sex (OR = 1.789 (1.527-2.097)), Body mass index (BMI) (OR = 1.019 (1.005-1.034)), and current smoking habits (OR = 1.246 (1.046-1.483)) were independent risk factors for TNs. Our findings indicate that there is a high prevalence of TNs in Beijing, with a higher prevalence in females than in males. Moreover, the prevalence increases as age increases. Smoking and BMI are

  4. The Prevalence of Thyroid Nodules and an Analysis of Related Lifestyle Factors in Beijing Communities

    PubMed Central

    Jiang, Hua; Tian, Yongfeng; Yan, Wenhua; Kong, Yue; Wang, Haibin; Wang, Anping; Dou, Jingtao; Liang, Ping; Mu, Yiming

    2016-01-01

    Thyroid nodules (TNs) have annual increasing trends worldwide, and large-scale investigations on the prevalence of TNs in Beijing communities have not been conducted since the introduction of salt iodization in 1995. We performed a cross-sectional study to determine the prevalence of TNs, their epidemiological characteristics, and their correlation with lifestyle factors. A total of 6324 permanent residents aged 18 years or older (mean age, 52.15 ± 11.58 years) from seven representative communities in Beijing were included in the analyses. Once informed consent was obtained, the subjects were asked to complete questionnaires, a physical examination, and thyroid ultrasound. A total of 3100 cases had TNs. The overall prevalence rate was 49.0%, and the age-standardized prevalence was 40.1%, which increased significantly as age increased (p < 0.001). The prevalence was significantly higher in females compared to males (p < 0.001), and it was significantly higher among female current smokers and former smokers compared to non-smokers (p = 0.007). There was no correlation between alcohol consumption and TNs, and there were no significant differences in the prevalence among different groups of taste preference. The prevalence decreased with an increased frequency of seafood intake (p = 0.015) and with higher literacy levels (p < 0.001). The Cochran–Armitage trend test showed that the prevalence significantly increased with decreased physical labor and exercise intensity (p < 0.001, p = 0.009). Logistic regression analysis showed that age (Odds ratio (OR) = 1.039 (1.034–1.044), p < 0.001), the female sex (OR = 1.789 (1.527–2.097)), Body mass index (BMI) (OR = 1.019 (1.005–1.034)), and current smoking habits (OR = 1.246 (1.046–1.483)) were independent risk factors for TNs. Our findings indicate that there is a high prevalence of TNs in Beijing, with a higher prevalence in females than in males. Moreover, the prevalence increases as age increases. Smoking and BMI

  5. Nonlinear Time Series Analysis of Nodulation Factor Induced Calcium Oscillations: Evidence for Deterministic Chaos?

    PubMed Central

    Hazledine, Saul; Sun, Jongho; Wysham, Derin; Downie, J. Allan; Oldroyd, Giles E. D.; Morris, Richard J.

    2009-01-01

    Legume plants form beneficial symbiotic interactions with nitrogen fixing bacteria (called rhizobia), with the rhizobia being accommodated in unique structures on the roots of the host plant. The legume/rhizobial symbiosis is responsible for a significant proportion of the global biologically available nitrogen. The initiation of this symbiosis is governed by a characteristic calcium oscillation within the plant root hair cells and this signal is activated by the rhizobia. Recent analyses on calcium time series data have suggested that stochastic effects have a large role to play in defining the nature of the oscillations. The use of multiple nonlinear time series techniques, however, suggests an alternative interpretation, namely deterministic chaos. We provide an extensive, nonlinear time series analysis on the nature of this calcium oscillation response. We build up evidence through a series of techniques that test for determinism, quantify linear and nonlinear components, and measure the local divergence of the system. Chaos is common in nature and it seems plausible that properties of chaotic dynamics might be exploited by biological systems to control processes within the cell. Systems possessing chaotic control mechanisms are more robust in the sense that the enhanced flexibility allows more rapid response to environmental changes with less energetic costs. The desired behaviour could be most efficiently targeted in this manner, supporting some intriguing speculations about nonlinear mechanisms in biological signaling. PMID:19675679

  6. Evolutionary history shapes patterns of mutualistic benefit in Acacia-rhizobial interactions.

    PubMed

    Barrett, Luke G; Zee, Peter C; Bever, James D; Miller, Joseph T; Thrall, Peter H

    2016-07-01

    The ecological and evolutionary factors that drive the emergence and maintenance of variation in mutualistic benefit (i.e., the benefits provided by one partner to another) in mutualistic symbioses are not well understood. In this study, we evaluated the role that host and symbiont phylogeny might play in determining patterns of mutualistic benefit for interactions among nine species of Acacia and 31 strains of nitrogen-fixing rhizobial bacteria. Using phylogenetic comparative methods we compared patterns of variation in mutualistic benefit (host response to inoculation) to rhizobial phylogenies constructed from housekeeping and symbiosis genes; and a multigene host phylogeny. We found widespread genotype-by-genotype variation in patterns of plant growth. A relatively large component of this variation (21-28%) was strongly influenced by the interacting evolutionary histories of both partners, such that phylogenetically similar host species had similar growth responses when inoculated with phylogenetically similar rhizobia. We also found a relatively large nonphylogenetic effect for the average mutualistic benefit provided by rhizobia to plants, such that phylogenetic relatedness did not predict the overall benefit provided by rhizobia across all hosts. We conclude that phylogenetic relatedness should frequently predict patterns of mutualistic benefit in acacia-rhizobial mutualistic interactions; but that some mutualistic traits also evolve independently of the phylogenies. PMID:27241367

  7. Mutation in GDP-fucose synthesis genes of Sinorhizobium fredii alters Nod factors and significantly decreases competitiveness to nodulate soybeans.

    PubMed

    Lamrabet, Y; Bellogín, R A; Cubo, T; Espuny, R; Gil, A; Krishnan, H B; Megias, M; Ollero, F J; Pueppke, S G; Ruiz-Sainz, J E; Spaink, H P; Tejero-Mateo, P; Thomas-Oates, J; Vinardell, J M

    1999-03-01

    We mutagenized Sinorhizobium fredii HH103-1 with Tn5-B20 and screened about 2,000 colonies for increased beta-galactosidase activity in the presence of the flavonoid naringenin. One mutant, designated SVQ287, produces lipochitooligosaccharide Nod factors (LCOs) that differ from those of the parental strain. The nonreducing N-acetylglucosamine residues of all of the LCOs of mutant SVQ287 lack fucose and 2-O-methylfucose substituents. In addition, SVQ287 synthesizes an LCO with an unusually long, C20:1 fatty acyl side chain. The transposon insertion of mutant SVQ287 lies within a 1.1-kb HindIII fragment. This and an adjacent 2.4-kb HindIII fragment were sequenced. The sequence contains the 3' end of noeK, nodZ, and noeL (the gene interrupted by Tn5-B20), and the 5' end of nolK, all in the same orientation. Although each of these genes has a similarly oriented counterpart on the symbiosis plasmid of the broad-host-range Rhizobium sp. strain NGR234, there are significant differences in the noeK/nodZ intergenic region. Based on amino acid sequence homology, noeL encodes GDP-D-mannose dehydratase, an enzyme involved in the synthesis of GDP-L-fucose, and nolK encodes a NAD-dependent nucleotide sugar epimerase/dehydrogenase. We show that expression of the noeL gene is under the control of NodD1 in S. fredii and is most probably mediated by the nod box that precedes nodZ. Transposon insertion into neoL has two impacts on symbiosis with Williams soybean: nodulation rate is reduced slightly and competitiveness for nodulation is decreased significantly. Mutant SVQ287 retains its ability to form nitrogen-fixing nodules on other legumes, but final nodule number is attenuated on Cajanus cajan. PMID:10065558

  8. [Comparison of the adaptive potential for Rhizobium leguminosarum bv. viceae nodule bacterial populations isolated in natural ecosystems and agrocenoses].

    PubMed

    Kurchak, O N; Provorov, N A; Simarov, B V

    2011-04-01

    Polymorphism analysis was performed in Rhizobium leguminosarum bv. viceae populations isolated from geographically distant regions of Ukraine and Middle Asia. Examination of cultural, biochemical, and symbiotic traits revealed interpopulation differences, which were attributed to the difference in conditions between natural ecosystems and agrocenoses. Vetch has high species diversity and is not cultivated in Middle Asia, and the corresponding rhizobial population displayed higher genetic diversity and higher polymorphism of adaptive traits ensuring saprophytic development in soil and the rhizosphere, including melanin synthesis (35%) and active exopolysaccharide production (90%). Strains of the Ukrainian population had a lower exopolysaccharide production (10%), did not produce melanin, had higher herbicide resistance, and utilized glucose and succinate (main components of plant root exudation) as carbon sources. Strains capable of efficient symbiosis with Vicia villosa Roth. had a higher frequency in the Middle Asian than in the Ukrainian population, especially among strains isolated from soil (80 and 35%, respectively). In addition, strains of the Middle Asian population better competed for nodulation. It was assumed that the formation of rhizobial populations in vetch cultivation regions (Ukraine) is aimed at adaptation to ectosymbiotic (rhizospheric) interactions with plants and anthropogenic stress factors, while strains of the vetch original center (Middle Asia) are mostly adapted to the endosymbiotic interaction and to natural edaphic stress factors. PMID:21675237

  9. Monophyly of nodA and nifH Genes across Texan and Costa Rican Populations of Cupriavidus Nodule Symbionts▿

    PubMed Central

    Andam, Cheryl P.; Mondo, Stephen J.; Parker, Matthew A.

    2007-01-01

    nodA and nifH phylogenies for Cupriavidus nodule bacteria from native legumes in Texas and Costa Rica grouped all strains into a single clade nested among neotropical Burkholderia strains. Thus, Cupriavidus symbiotic genes were not acquired independently in different regions and are derived from other Betaproteobacteria rather than from α-rhizobial donors. PMID:17526782

  10. [Evolution of Root Nodule Bacteria: Reconstruction of the Speciation Processes Resulting from Genomic Rearrangements in a Symbiotic System].

    PubMed

    Provorov, N A; Andronov, E E

    2016-01-01

    The processes of speciation and macroevolution of root nodule bacteria (rhizobia), based on deep rearrangements of their genomes and occurring in the N₂-fixing symbiotic system, are reconstructed. At the first stage of rhizobial evolution, transformation of free-living diazotrophs (related to Rhodopseudomonas) to symbiotic N₂-fixers (Bradyrhizobium) occurred due to the acquisition of the fix gene system, which is responsible for providing nitrogenase with electrons and reducing equivalents, as well as for oxygen-dependent regulation of nitrogenase synthesis in planta, and then of the nod genes responsible for the synthesis of the lipo- chito-oligosaccharide Nod factors, which induce root nodule development. The subsequent rearrangements of bacterial genomes included: (1) increased volume of hereditary information supported by species, genera (pan-genome), and individual strains; (2) transition from the unitary genome to a multicomponent one; and (3) enhanced levels of bacterial genetic plasticity and horizontal gene transfer, resulting in formation of new genera, of which Mesorhizobium, Rhizobium, and Sinorhizobium are the largest, and of over 100 species. Rhizobial evolution caused by development and diversification of the Nod factor synthesizing systems may result in both increased host specificity range (transition of Bradyrhizobium from autotrophic to symbiotrophic carbon metabolism in interaction with a broad spectrum of legumes) and to its contraction (transition of Rhizobium and Sinorhizobium to "altruistic" interaction with legumes of the galegoid clade). Reconstruction of the evolutionary pathway from symbiotic N₂-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supracpecies complexes, ratios of the macro- and microevolutionary mechanisms, and developmetn of cooperative adaptations based on altruistic

  11. New aspect of plant–rhizobia interaction: Alkaloid biosynthesis in Crotalaria depends on nodulation

    PubMed Central

    Irmer, Simon; Podzun, Nora; Langel, Dorothee; Heidemann, Franziska; Kaltenegger, Elisabeth; Schemmerling, Brigitte; Geilfus, Christoph-Martin; Zörb, Christian; Ober, Dietrich

    2015-01-01

    Infection of legume hosts by rhizobial bacteria results in the formation of a specialized organ, the nodule, in which atmospheric nitrogen is reduced to ammonia. Nodulation requires the reprogramming of the plant cell, allowing the microsymbiont to enter the plant tissue in a highly controlled manner. We have found that, in Crotalaria (Fabaceae), this reprogramming is associated with the biosynthesis of pyrrolizidine alkaloids (PAs). These compounds are part of the plant’s chemical defense against herbivores and cannot be regarded as being functionally involved in the symbiosis. PAs in Crotalaria are detectable only when the plants form nodules after infection with their rhizobial partner. The identification of a plant-derived sequence encoding homospermidine synthase (HSS), the first pathway-specific enzyme of PA biosynthesis, suggests that the plant and not the microbiont is the producer of PAs. Transcripts of HSS are detectable exclusively in the nodules, the tissue with the highest concentration of PAs, indicating that PA biosynthesis is restricted to the nodules and that the nodules are the source from which the alkaloids are transported to the above ground parts of the plant. The link between nodulation and the biosynthesis of nitrogen-containing alkaloids in Crotalaria highlights a further facet of the effect of symbiosis with rhizobia on the ecologically important trait of the plant’s chemical defense. PMID:25775562

  12. GS52 Ecto-Apyrase Plays a Critical Role during Soybean Nodulation1[W][OA

    PubMed Central

    Govindarajulu, Manjula; Kim, Sung-Yong; Libault, Marc; Berg, R. Howard; Tanaka, Kiwamu; Stacey, Gary; Taylor, Christopher G.

    2009-01-01

    Apyrases are non-energy-coupled nucleotide phosphohydrolases that hydrolyze nucleoside triphosphates and nucleoside diphosphates to nucleoside monophosphates and orthophosphates. GS52, a soybean (Glycine soja) ecto-apyrase, was previously shown to be induced very early in response to inoculation with the symbiotic bacterium Bradyrhizobium japonicum. Overexpression of the GS52 ecto-apyrase in Lotus japonicus increased the level of rhizobial infection and enhanced nodulation. These data suggest a critical role for the GS52 ecto-apyrase during nodulation. To further investigate the role of GS52 during nodulation, we used RNA interference to silence GS52 expression in soybean (Glycine max) roots using Agrobacterium rhizogenes-mediated root transformation. Transcript levels of GS52 were significantly reduced in GS52 silenced roots and these roots exhibited reduced numbers of mature nodules. Development of the nodule primordium and subsequent nodule maturation was significantly suppressed in GS52 silenced roots. Transmission electron micrographs of GS52 silenced root nodules showed that early senescence and infected cortical cells were devoid of symbiosome-containing bacteroids. Application of exogenous adenosine diphosphate to silenced GS52 roots restored nodule development. Restored nodules contained bacteroids, thus indicating that extracellular adenosine diphosphate is important during nodulation. These results clearly suggest that GS52 ecto-apyrase catalytic activity is critical for the early B. japonicum infection process, initiation of nodule primordium development, and subsequent nodule organogenesis in soybean. PMID:19036836

  13. Methylotrophic Methylobacterium Bacteria Nodulate and Fix Nitrogen in Symbiosis with Legumes

    PubMed Central

    Sy, Abdoulaye; Giraud, Eric; Jourand, Philippe; Garcia, Nelly; Willems, Anne; de Lajudie, Philippe; Prin, Yves; Neyra, Marc; Gillis, Monique; Boivin-Masson, Catherine; Dreyfus, Bernard

    2001-01-01

    Rhizobia described so far belong to three distinct phylogenetic branches within the α-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, “Methylobacterium nodulans,” within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the α subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that “M. nodulans” is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that “M. nodulans” NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer. PMID:11114919

  14. Population Genomics Analysis of Legume Host Preference for Specific Rhizobial Genotypes in the Rhizobium leguminosarum bv. viciae Symbioses.

    PubMed

    Jorrin, Beatriz; Imperial, Juan

    2015-03-01

    Rhizobium leguminosarum bv. viciae establishes root nodule symbioses with several legume genera. Although most isolates are equally effective in establishing symbioses with all host genera, previous evidence suggests that hosts select specific rhizobial genotypes among those present in the soil. We have used population genomics to further investigate this observation. Pisum sativum, Lens culinaris, Vicia sativa, and V. faba plants were used to trap rhizobia from a well-characterized soil, and pooled genomic DNA from 100 isolates from each plant were sequenced. Sequence reads were aligned to the R. leguminosarum bv. viciae 3841 reference genome. High overall conservation of sequences was observed in all subpopulations, although several multigenic regions were absent from the soil population. A large fraction (16 to 22%) of sequence reads could not be recruited to the reference genome, suggesting that they represent sequences specific to that particular soil population. Although highly conserved, the 16S to 23S ribosomal RNA gene region presented single nucleotide polymorphisms (SNP) regarding the reference genome, but no striking differences could be found among plant-selected subpopulations. Plant-specific SNP patterns were, however, clearly observed within the nod gene cluster, supporting the existence of a plant preference for specific rhizobial genotypes. This was also shown after genome-wide analysis of SNP patterns. PMID:25514682

  15. Enhanced nodulation of peanut when co-inoculated with fungal endophyte Phomopsis liquidambari and bradyrhizobium.

    PubMed

    Zhang, Wei; Wang, Hong-Wei; Wang, Xing-Xiang; Xie, Xing-Guang; Siddikee, Md Ashaduzzaman; Xu, Ri-Sheng; Dai, Chuan-Chao

    2016-01-01

    In peanut continuous cropping soil, the application of fungal endophyte Phomopsis liquidambari B3 showed peanut pod yield promotion and root nodule number increase. P. liquidambari improved soil environment by degrading allelochemicals and thus promoted peanut pod yield. Furthermore, peanut yield promotion is in part due to the root nodule increase since nodular nitrogen fixation provides the largest source of nitrogen for peanut. However, it is unknown whether this nodule number increase is induced by fungal endophyte. We therefore conducted several pot experiments using vermiculite to investigate the effects of P. liquidambari on peanut-bradyrhizobium nodulation. Our results showed that P. liquidambari co-inoculated with bradyrhizobium increased root nodule number and shoot accumulated nitrogen by 28.25% and 29.71%, respectively. Nodulation dynamics analysis showed that P. liquidambari accelerated nodule initiation and subsequent nodule development. Meanwhile, P. liquidambari was able to colonize the peanut root as an endophyte. The dynamics of P. liquidambari and bradyrhizobial root colonization analysis showed that P. liquidambari inoculation significantly increased the rate of bradyrhizobial colonization. Furthermore, P. liquidambari inoculation significantly increased flavonoids synthesis-related enzymes activities, two common types of flavonoid (luteolin and quercetin-peanut rhizobial nod gene inducer) secretion and lateral root (peanut rhizobial infection site) formation, indicating that P. liquidambari altered the peanut nodulation-related physiological and metabolic activities. These obtained results confirmed the direct contribution of P. liquidambari in enhancing peanut-bradyrhizobium interaction, nodulation and yield. PMID:26584395

  16. A novel ARID DNA-binding protein interacts with SymRK and is expressed during early nodule development in Lotus japonicus.

    PubMed

    Zhu, Hui; Chen, Tao; Zhu, Maosheng; Fang, Qing; Kang, Heng; Hong, Zonglie; Zhang, Zhongming

    2008-09-01

    During the establishment of symbiosis in legume roots, the rhizobial Nod factor signal is perceived by the host cells via receptor-like kinases, including SymRK. The NODULE INCEPTION (NIN) gene in Lotus japonicus is required for rhizobial entry into root cells and for nodule organogenesis. We describe here a novel DNA-binding protein from L. japonicus, referred to as SIP1, because it was identified as a SymRK-interacting protein. SIP1 contains a conserved AT-rich interaction domain (ARID) and represents a unique member of the ARID-containing proteins in plants. The C terminus of SIP1 was found to be responsible for its interaction with the kinase domain of SymRK and for homodimerization in the absence of DNA. SIP1 specifically binds to the promoter of LjNIN but not to that of LjCBP1 (a calcium-binding protein gene), both of which are known to be inducible by Nod factors. SIP1 recognizes two of the three AT-rich domains present in the NIN gene promoter. Deletion of one of the AT-rich domains at the NIN promoter diminishes the binding of SIP1 to the NIN promoter. The protein is localized to the nuclei when expressed as a red fluorescence fusion protein in the onion (Allium cepa) epidermal cells. The SIP1 gene is expressed constitutively in the uninfected roots, and its expression levels are elevated after infection by Mesorhizobium loti. It is proposed that SIP1 may be required for the expression of NIN and involved in the initial communications between the rhizobia and the host root cells. PMID:18633121

  17. RAPD-inferred genetic variability of some indigenous Rhizobium leguminosarum isolates from red clover (Trifolium pratense L.) nodules.

    PubMed

    Stefan, Andrei; Rosu, Craita M; Stedel, Catalina; Gorgan, Lucian D; Efrose, Rodica C

    2015-09-01

    The application of commercial rhizobial inoculants to legume crops is proving to be an alternative to synthetic fertilizer use. The challenge for sustainable agriculture resides in the compatibility between crop, inoculants and environmental conditions. The evaluation of symbiotic efficiency and genetic diversity of indigenous rhizobial strains could lead to the development of better inoculants and increased crop production. The genetic variability of 32 wild indigenous rhizobial isolates was assessed by RAPD (Random Amplified Polymorphic DNA). The strains were isolated from red clover (Trifolium pratense L.) nodules from two distinct geographical regions of Northern and Eastern Romania. Three decamer primers were used to resolve the phylogenetic relationships between the investigated isolates. Cluster analysis revealed a high diversity; most strains clustered together based on their geographical location. PMID:26344027

  18. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

    PubMed Central

    Young, Nevin D.; Debellé, Frédéric; Oldroyd, Giles E. D.; Geurts, Rene; Cannon, Steven B.; Udvardi, Michael K.; Benedito, Vagner A.; Mayer, Klaus F. X.; Gouzy, Jérôme; Schoof, Heiko; Van de Peer, Yves; Proost, Sebastian; Cook, Douglas R.; Meyers, Blake C.; Spannagl, Manuel; Cheung, Foo; De Mita, Stéphane; Krishnakumar, Vivek; Gundlach, Heidrun; Zhou, Shiguo; Mudge, Joann; Bharti, Arvind K.; Murray, Jeremy D.; Naoumkina, Marina A.; Rosen, Benjamin; Silverstein, Kevin A. T.; Tang, Haibao; Rombauts, Stephane; Zhao, Patrick X.; Zhou, Peng; Barbe, Valérie; Bardou, Philippe; Bechner, Michael; Bellec, Arnaud; Berger, Anne; Bergès, Hélène; Bidwell, Shelby; Bisseling, Ton; Choisne, Nathalie; Couloux, Arnaud; Denny, Roxanne; Deshpande, Shweta; Dai, Xinbin; Doyle, Jeff; Dudez, Anne-Marie; Farmer, Andrew D.; Fouteau, Stéphanie; Franken, Carolien; Gibelin, Chrystel; Gish, John; Goldstein, Steven; González, Alvaro J.; Green, Pamela J.; Hallab, Asis; Hartog, Marijke; Hua, Axin; Humphray, Sean; Jeong, Dong-Hoon; Jing, Yi; Jöcker, Anika; Kenton, Steve M.; Kim, Dong-Jin; Klee, Kathrin; Lai, Hongshing; Lang, Chunting; Lin, Shaoping; Macmil, Simone L; Magdelenat, Ghislaine; Matthews, Lucy; McCorrison, Jamison; Monaghan, Erin L.; Mun, Jeong-Hwan; Najar, Fares Z.; Nicholson, Christine; Noirot, Céline; O’Bleness, Majesta; Paule, Charles R.; Poulain, Julie; Prion, Florent; Qin, Baifang; Qu, Chunmei; Retzel, Ernest F.; Riddle, Claire; Sallet, Erika; Samain, Sylvie; Samson, Nicolas; Sanders, Iryna; Saurat, Olivier; Scarpelli, Claude; Schiex, Thomas; Segurens, Béatrice; Severin, Andrew J.; Sherrier, D. Janine; Shi, Ruihua; Sims, Sarah; Singer, Susan R.; Sinharoy, Senjuti; Sterck, Lieven; Viollet, Agnès; Wang, Bing-Bing; Wang, Keqin; Wang, Mingyi; Wang, Xiaohong; Warfsmann, Jens; Weissenbach, Jean; White, Doug D.; White, Jim D.; Wiley, Graham B.; Wincker, Patrick; Xing, Yanbo; Yang, Limei; Yao, Ziyun; Ying, Fu; Zhai, Jixian; Zhou, Liping; Zuber, Antoine; Dénarié, Jean; Dixon, Richard A.; May, Gregory D.; Schwartz, David C.; Rogers, Jane; Quétier, Francis; Town, Christopher D.; Roe, Bruce A.

    2011-01-01

    Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation 1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Mya). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species 2. Medicago truncatula (Mt) is a long-established model for the study of legume biology. Here we describe the draft sequence of the Mt euchromatin based on a recently completed BAC-assembly supplemented with Illumina-shotgun sequence, together capturing ~94% of all Mt genes. A whole-genome duplication (WGD) approximately 58 Mya played a major role in shaping the Mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the Mt genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max (Gm) and Lotus japonicus (Lj). Mt is a close relative of alfalfa (M. sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the Mt genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox. PMID:22089132

  19. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation.

    PubMed

    Qiu, Liping; Lin, Jie-Shun; Xu, Ji; Sato, Shusei; Parniske, Martin; Wang, Trevor L; Downie, J Allan; Xie, Fang

    2015-10-01

    Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor. PMID:26517270

  20. SCARN a Novel Class of SCAR Protein That Is Required for Root-Hair Infection during Legume Nodulation

    PubMed Central

    Qiu, Liping; Lin, Jie-shun; Xu, Ji; Sato, Shusei; Parniske, Martin; Wang, Trevor L.; Downie, J. Allan; Xie, Fang

    2015-01-01

    Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-terminal domains of SCAR proteins interact with other components of the SCAR/WAVE complex. The conserved C-terminal domains of SCAR proteins bind to and activate the actin-related protein 2/3 (ARP2/3) complex, which can bind to actin filaments catalyzing new actin filament formation by nucleating actin branching. We have identified, SCARN (SCAR-Nodulation), a gene required for root hair infection of Lotus japonicus by Mesorhizobium loti. Although the SCARN protein is related to Arabidopsis thaliana SCAR2 and SCAR4, it belongs to a distinct legume-sub clade. We identified other SCARN-like proteins in legumes and phylogeny analyses suggested that SCARN may have arisen from a gene duplication and acquired specialized functions in root nodule symbiosis. Mutation of SCARN reduced formation of infection-threads and their extension into the root cortex and slightly reduced root-hair length. Surprisingly two of the scarn mutants showed constitutive branching of root hairs in uninoculated plants. However we observed no effect of scarn mutations on trichome development or on the early actin cytoskeletal accumulation that is normally seen in root hair tips shortly after M. loti inoculation, distinguishing them from other symbiosis mutations affecting actin nucleation. The C-terminal domain of SCARN binds to ARPC3 and ectopic expression of the N-terminal SCAR-homology domain (but not the full length protein) inhibited nodulation. In addition, we found that SCARN expression is enhanced by M. loti in epidermal cells and that this is directly regulated by the NODULE INCEPTION (NIN) transcription factor. PMID:26517270

  1. Lipo-chitooligosaccharidic nodulation factors and their perception by plant receptors.

    PubMed

    Fliegmann, Judith; Bono, Jean-Jacques

    2015-10-01

    Lipo-chitooligosaccharides produced by nitrogen-fixing rhizobia are signaling molecules involved in the establishment of an important agronomical and ecological symbiosis with plants. These compounds, known as Nod factors, are biologically active on plant roots at very low concentrations indicating that they are perceived by specific receptors. This article summarizes the main strategies developed for the syntheses of bioactive Nod factors and their derivatives in order to better understand their mode of perception. Different Nod factor receptors and LCO-binding proteins identified by genetic or biochemical approaches are also presented, indicating perception mechanisms that seem to be more complicated than expected, probably involving multi-component receptor complexes. PMID:26233756

  2. MicroRNA167-Directed Regulation of the Auxin Response Factors GmARF8a and GmARF8b Is Required for Soybean Nodulation and Lateral Root Development.

    PubMed

    Wang, Youning; Li, Kexue; Chen, Liang; Zou, Yanmin; Liu, Haipei; Tian, Yinping; Li, Dongxiao; Wang, Rui; Zhao, Fang; Ferguson, Brett J; Gresshoff, Peter M; Li, Xia

    2015-07-01

    Legume root nodules convert atmospheric nitrogen gas into ammonium through symbiosis with a prokaryotic microsymbiont broadly called rhizobia. Auxin signaling is required for determinant nodule development; however, the molecular mechanism of auxin-mediated nodule formation remains largely unknown. Here, we show in soybean (Glycine max) that the microRNA miR167 acts as a positive regulator of lateral root organs, namely nodules and lateral roots. miR167c expression was up-regulated in the vasculature, pericycle, and cortex of soybean roots following inoculation with Bradyrhizobium japonicum strain USDA110 (the microsymbiont). It was found to positively regulate nodule numbers directly by repressing the target genes GmARF8a and GmARF8b (homologous genes of Arabidopsis [Arabidopsis thaliana] AtARF8 that encode auxin response factors). Moreover, the expression of miR167 and its targets was up- and down-regulated by auxin, respectively. The miR167-GmARF8 module also positively regulated nodulation efficiency under low microsymbiont density, a condition often associated with environmental stress. The regulatory role of miR167 on nodule initiation was dependent on the Nod factor receptor GmNFR1α, and it acts upstream of the nodulation-associated genes nodule inception, nodulation signaling pathway1, early nodulin40-1, NF-YA1 (previously known as HAEM activator protein2-1), and NF-YA2. miR167 also promoted lateral root numbers. Collectively, our findings establish a key role for the miR167-GmARF8 module in auxin-mediated nodule and lateral root formation in soybean. PMID:25941314

  3. Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum

    PubMed Central

    Elliott, Geoffrey N.; Chen, Wen-Ming; Bontemps, Cyril; Chou, Jui-Hsing; Young, J. Peter W.; Sprent, Janet I.; James, Euan K.

    2007-01-01

    Background and Aims Species of the genus Burkholderia, from the Betaproteobacteria, have been isolated from legume nodules, but so far they have only been shown to form symbioses with species of Mimosa, sub-family Mimosoideae. This work investigates whether Burkholderia tuberum strains STM678 (isolated from Aspalathus carnosa) and DUS833 (from Aspalathus callosa) can nodulate species of the South African endemic papilionoid genera Cyclopia (tribe Podalyrieae) and Aspalathus (Crotalarieae) as well as the promiscuous legume Macroptilium atropurpureum (Phaseoleae). Method Bacterial strains and the phylogeny of their symbiosis-related (nod) genes were examined via 16S rRNA gene sequencing. Seedlings were grown in liquid culture and inoculated with one of the two strains of B. tuberum or with Sinorhizobium strain NGR 234 (from Lablab purpureus), Mesorhizobium strain DUS835 (from Aspalathus linearis) or Methylobacterium nodulans (from Crotalaria podocarpa). Some nodules, inoculated with green fluorescence protein (GFP)-tagged strains, were examined by light and electron microscopy coupled with immunogold labelling with a Burkholderia-specific antibody. The presence of active nitrogenase was checked by immunolabelling of nitrogenase and by the acetylene reduction assay. B. tuberum STM678 was also tested on a wide range of legumes from all three sub-families. Key Results Nodules were not formed on any of the Aspalathus spp. Only B. tuberum nodulated Cyclopia falcata, C. galioides, C. genistoides, C. intermedia and C. pubescens. It also effectively nodulated M. atropurpureum but no other species tested. GFP-expressing inoculant strains were located inside infected cells of C. genistoides, and bacteroids in both Cyclopia spp. and M. atropurpureum were immunogold-labelled with antibodies against Burkholderia and nitrogenase. Nitrogenase activity was also shown using the acetylene reduction assay. This is the first demonstration that a β-rhizobial strain can effectively

  4. Thyroid nodules.

    PubMed

    Niedziela, Marek

    2014-03-01

    According to the literature, thyroid nodules (TNs) are quite rare in the first two decades of life and are predominantly non-cancerous, although cancerous TNs are more common in the first two decades of life than in adults. Therefore, it is important for clinicians to distinguish benign from malignant lesions preoperatively because the latter require a total thyroidectomy with or without neck lymph node dissection. A careful work-up and a fine-needle aspiration biopsy (FNAB) are mandatory to improve the preoperative diagnosis. High-resolution thyroid ultrasound and real-time elastosonography are adjuvant presurgical tools in selecting patients for surgery, particularly those with indeterminate or non-diagnostic cytology. Elevated thyroid-stimulating hormone (TSH) level in a patient with a thyroid nodule is a new laboratory predictor of thyroid cancer risk. The majority of thyroid carcinomas derive from the follicular cell, whereas medullary thyroid carcinoma (MTC) derives from calcitonin-producing cells. Patients with MTC are screened for germ-line RET mutations to detect carriers and identify family members for prophylactic or therapeutic thyroidectomy. PMID:24629865

  5. Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals1[OPEN

    PubMed Central

    Larrainzar, Estíbaliz; Riely, Brendan K.; Kim, Sang Cheol; Carrasquilla-Garcia, Noelia; Yu, Hee-Ju; Hwang, Hyun-Ju; Oh, Mijin; Kim, Goon Bo; Surendrarao, Anandkumar K.; Chasman, Deborah; Siahpirani, Alireza F.; Penmetsa, Ramachandra V.; Lee, Gang-Seob; Kim, Namshin; Roy, Sushmita; Mun, Jeong-Hwan; Cook, Douglas R.

    2015-01-01

    The legume-rhizobium symbiosis is initiated through the activation of the Nodulation (Nod) factor-signaling cascade, leading to a rapid reprogramming of host cell developmental pathways. In this work, we combine transcriptome sequencing with molecular genetics and network analysis to quantify and categorize the transcriptional changes occurring in roots of Medicago truncatula from minutes to days after inoculation with Sinorhizobium medicae. To identify the nature of the inductive and regulatory cues, we employed mutants with absent or decreased Nod factor sensitivities (i.e. Nodulation factor perception and Lysine motif domain-containing receptor-like kinase3, respectively) and an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant (sickle). This unique data set encompasses nine time points, allowing observation of the symbiotic regulation of diverse biological processes with high temporal resolution. Among the many outputs of the study is the early Nod factor-induced, ET-regulated expression of ET signaling and biosynthesis genes. Coupled with the observation of massive transcriptional derepression in the ET-insensitive background, these results suggest that Nod factor signaling activates ET production to attenuate its own signal. Promoter:β-glucuronidase fusions report ET biosynthesis both in root hairs responding to rhizobium as well as in meristematic tissue during nodule organogenesis and growth, indicating that ET signaling functions at multiple developmental stages during symbiosis. In addition, we identified thousands of novel candidate genes undergoing Nod factor-dependent, ET-regulated expression. We leveraged the power of this large data set to model Nod factor- and ET-regulated signaling networks using MERLIN, a regulatory network inference algorithm. These analyses predict key nodes regulating the biological process impacted by Nod factor perception. We have made these results available to the research community through a searchable online

  6. Transforming Growth Factor β1 Could Influence Thyroid Nodule Elasticity and Also Improve Cervical Lymph Node Metastasis in Papillary Thyroid Carcinoma.

    PubMed

    Li, Yi; Wang, Yan; Wu, Qiong; Hu, Bing

    2015-11-01

    Ultrasound elastography has been a very useful tool in predicting the risk of malignant thyroid tumor for several years. The objective of this study was to determine if there is a correlation between strain ratio (SR), collagen deposition and transforming growth factor β1 (TGF-β1) expression in different types of thyroid nodules and if TGF-β1 is related to cervical lymph node metastasis. 102 nodules from 81 patients who underwent thyroid resection surgery in our hospital were retrospectively studied. All of these patients had undergone ultrasound elastography scanning before surgery. Masson staining and immunohistochemical staining were used to evaluate the ratio of expression of collagen deposition and TGF-β1. There was a significant difference between benign and malignant thyroid nodules in SR (8.913 ± 11.021 vs. 1.732 ± 0.727, p = 0.000), collagen content (0.371 ± 0.125 vs. 0.208 ± 0.057, p = 0.000) and TGF-β1 expression (0.336 ± 0.093 vs. 0.178 ± 0.071, p = 0.000). A cutoff of 2.99 for SR measurement was selected for the highest Youden index for predicting malignant thyroid nodules, which yielded 87.88% sensitivity, 100% specificity, 100% positive predictive value, 83.72% negative predictive value and 92.15% accuracy. Expression of collagen and TGF-β1 was positively correlated with SR measurements (coefficient = 0.839 for collagen and 0.855 for TGF-β1, p = 0.000). Among 61 nodules with papillary thyroid carcinoma, the average SR for the metastasis group was higher than that for the non-metastasis group (10.955 ± 13.805 and 7.852 ± 7.931, respectively), but without statistical significance (p = 0.287). Collagen deposition was significantly higher in the metastasis group than in the non-metastasis group (0.421 ± 0.091 vs. 0.353 ± 0.118, p = 0.011). TGF-β1 expression was also significantly higher in the metastasis group than in the non-metastasis group (0.378 ± 0.0.69 vs. 0.328 ± 0.091, p = 0.016). To conclude, TGF-β1 may contribute to thyroid

  7. Novel and Convenient Method to Evaluate the Character of Solitary Pulmonary Nodule-Comparison of Three Mathematical Prediction Models and Further Stratification of Risk Factors

    PubMed Central

    Xiao, Fei; Liu, Deruo; Guo, Yongqing; Shi, Bin; Song, Zhiyi; Tian, Yanchu; Liang, Chaoyang

    2013-01-01

    Objective To study risk factors that affect the evaluation of malignancy in patients with solitary pulmonary nodules (SPN) and verify different predictive models for malignant probability of SPN. Methods Retrospectively analyzed 107 cases of SPN with definite post-operative histological diagnosis whom underwent surgical procedures in China-Japan Friendship Hospital from November of 2010 to February of 2013. Age, gender, smoking history, malignancy history of patients, imaging features of the nodule including maximum diameter, position, spiculation, lobulation, calcification and serum level of CEA and Cyfra21-1 were assessed as potential risk factors. Univariate analysis model was used to establish statistical correlation between risk factors and post-operative histological diagnosis. Receiver operating characteristic (ROC) curves were drawn using different predictive models for malignant probability of SPN to get areas under the curves (AUC values), sensitivity, specificity, positive predictive values, negative predictive values for each model, respectively. The predictive effectiveness of each model was statistically assessed subsequently. Results In 107 patients, 78 cases were malignant (72.9%), 29 cases were benign (27.1%). Statistical significant difference was found between benign and malignant group in age, maximum diameter, serum level of Cyfra21-1, spiculation, lobulation and calcification of the nodules. The AUC values were 0.786±0.053 (Mayo model), 0.682±0.060 (VA model) and 0.810±0.051 (Peking University People’s Hospital model), respectively. Conclusions Serum level of Cyfra21-1, patient’s age, maximum diameter of the nodule, spiculation, lobulation and calcification of the nodule are independent risk factors associated with the malignant probability of SPN. Peking University People’s Hospital model is of high accuracy and clinical value for patients with SPN. Adding serum index (e.g. Cyfra21-1) into the prediction models as a new risk factor

  8. Diverse novel mesorhizobia nodulate New Zealand native Sophora species.

    PubMed

    Tan, Heng Wee; Heenan, Peter B; De Meyer, Sofie E; Willems, Anne; Andrews, Mitchell

    2015-03-01

    Forty eight rhizobial isolates from New Zealand (NZ) native Sophora spp. growing in natural ecosystems were characterised. Thirty eight isolates across five groups showed greatest similarity to Mesorhizobium ciceri LMG 14989(T) with respect to their 16S rRNA and concatenated recA, glnll and rpoB sequences. Seven isolates had a 16S rRNA sequence identical to M. amorphae ATCC 19665(T) but showed greatest similarity to M. septentrionale LMG 23930(T) on their concatenated recA, glnll and rpoB sequences. All isolates grouped closely together for their nifH, nodA and nodC sequences, clearly separate from all other rhizobia in the GenBank database. None of the type strains closest to the Sophora isolates based on 16S rRNA sequence similarity nodulated Sophora microphylla but they all nodulated their original host. Twenty one Sophora isolates selected from the different 16S rRNA groupings produced N2-fixing nodules on three Sophora spp. but none nodulated any host of the type strains for the related species. DNA hybridisations indicated that these isolates belong to novel Mesorhizobium spp. that nodulate NZ native Sophora species. PMID:25498849

  9. South African Papilionoid Legumes Are Nodulated by Diverse Burkholderia with Unique Nodulation and Nitrogen-Fixation Loci

    PubMed Central

    Beukes, Chrizelle W.; Venter, Stephanus N.; Law, Ian J.; Phalane, Francina L.; Steenkamp, Emma T.

    2013-01-01

    The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region. PMID:23874611

  10. Enzymatic Activity of the Soybean Ecto-Apyrase GS52 Is Essential for Stimulation of Nodulation1[W][OA

    PubMed Central

    Tanaka, Kiwamu; Nguyen, Cuong T.; Libault, Marc; Cheng, Jianlin; Stacey, Gary

    2011-01-01

    Nitrogen is an essential nutrient for plant growth. In the Rhizobium-legume symbiosis, root nodules are the sites of bacterial nitrogen fixation, in which atmospheric nitrogen is converted into a form that plants can utilize. While recent studies suggested an important role for the soybean (Glycine max) ecto-apyrase GS52 in rhizobial root hair infection and root nodule formation, precisely how this protein impacts the nodulation process remains undetermined. In this study, the biochemical characteristics of the GS52 enzyme were investigated. Computer modeling of the GS52 apyrase structure identified key amino acid residues important for catalytic activity, which were subsequently mutagenized. Although the GS52 enzyme exhibited broad substrate specificity, its activity on pyrimidine nucleotides and diphosphate nucleotides was significantly higher than on ATP. This result was corroborated by structural modeling of GS52, which predicted a low specificity for the adenine base within the substrate-binding pocket of the enzyme. The wild-type enzyme and its inactive mutant forms were expressed in soybean roots in order to evaluate the importance of GS52 enzymatic activity for nodulation. The results indicated a clear correlation between GS52 enzymatic activity and nodule number. Altogether, our study indicates that the catalytic activity of the GS52 apyrase, likely acting on extracellular nucleotides, is critical for rhizobial infection and nodulation. PMID:21346172

  11. Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the southern African crotalarioid clade Lotononis s.l.

    PubMed Central

    Ardley, Julie K.; Reeve, Wayne G.; O'Hara, Graham W.; Yates, Ron J.; Dilworth, Michael J.; Howieson, John G.

    2013-01-01

    Background and Aims The legume clade Lotononis sensu lato (s.l.; tribe Crotalarieae) comprises three genera: Listia, Leobordea and Lotononis sensu stricto (s.s.). Listia species are symbiotically specific and form lupinoid nodules with rhizobial species of Methylobacterium and Microvirga. This work investigated whether these symbiotic traits were confined to Listia by determining the ability of rhizobial strains isolated from species of Lotononis s.l. to nodulate Listia, Leobordea and Lotononis s.s. hosts and by examining the morphology and structure of the resulting nodules. Methods Rhizobia were characterized by sequencing their 16S rRNA and nodA genes. Nodulation and N2 fixation on eight taxonomically diverse Lotononis s.l. species were determined in glasshouse trials. Nodules of all hosts, and the process of infection and nodule initiation in Listia angolensis and Listia bainesii, were examined by light microscopy. Key Results Rhizobia associated with Lotononis s.l. were phylogenetically diverse. Leobordea and Lotononis s.s. isolates were most closely related to Bradyrhizobium spp., Ensifer meliloti, Mesorhizobium tianshanense and Methylobacterium nodulans. Listia angolensis formed effective nodules only with species of Microvirga. Listia bainesii nodulated only with pigmented Methylobacterium. Five lineages of nodA were found. Listia angolensis and L. bainesii formed lupinoid nodules, whereas nodules of Leobordea and Lotononis s.s. species were indeterminate. All effective nodules contained uniformly infected central tissue. Listia angolensis and L. bainesii nodule initials occurred on the border of the hypocotyl and along the tap root, and nodule primordia developed in the outer cortical layer. Neither root hair curling nor infection threads were seen. Conclusions Two specificity groups occur within Lotononis s.l.: Listia species are symbiotically specific, while species of Leobordea and Lotononis s.s. are generally promiscuous and interact with rhizobia of

  12. A Novel Sucrose-Regulatory MADS-Box Transcription Factor GmNMHC5 Promotes Root Development and Nodulation in Soybean (Glycine max [L.] Merr.)

    PubMed Central

    Liu, Wei; Han, Xiangdong; Zhan, Ge; Zhao, Zhenfang; Feng, Yongjun; Wu, Cunxiang

    2015-01-01

    The MADS-box protein family includes many transcription factors that have a conserved DNA-binding MADS-box domain. The proteins in this family were originally recognized to play prominent roles in floral development. Recent findings, especially with regard to the regulatory roles of the AGL17 subfamily in root development, have greatly broadened their known functions. In this study, a gene from soybean (Glycine max [L.] Merr.), GmNMHC5, was cloned from the Zigongdongdou cultivar and identified as a member of the AGL17 subfamily. Real-time fluorescence quantitative PCR analysis showed that GmNMHC5 was expressed at much higher levels in roots and nodules than in other organs. The activation of expression was first examined in leaves and roots, followed by shoot apexes. GmNMHC5 expression levels rose sharply when the plants were treated under short-day conditions (SD) and started to pod, whereas low levels were maintained in non-podding plants under long-day conditions (LD). Furthermore, overexpression of GmNMHC5 in transgenic soybean significantly promoted lateral root development and nodule building. Moreover, GmNMHC5 is upregulated by exogenous sucrose. These results indicate that GmNMHC5 can sense the sucrose signal and plays significant roles in lateral root development and nodule building. PMID:26404246

  13. A Novel Sucrose-Regulatory MADS-Box Transcription Factor GmNMHC5 Promotes Root Development and Nodulation in Soybean (Glycine max [L.] Merr.).

    PubMed

    Liu, Wei; Han, Xiangdong; Zhan, Ge; Zhao, Zhenfang; Feng, Yongjun; Wu, Cunxiang

    2015-01-01

    The MADS-box protein family includes many transcription factors that have a conserved DNA-binding MADS-box domain. The proteins in this family were originally recognized to play prominent roles in floral development. Recent findings, especially with regard to the regulatory roles of the AGL17 subfamily in root development, have greatly broadened their known functions. In this study, a gene from soybean (Glycine max [L.] Merr.), GmNMHC5, was cloned from the Zigongdongdou cultivar and identified as a member of the AGL17 subfamily. Real-time fluorescence quantitative PCR analysis showed that GmNMHC5 was expressed at much higher levels in roots and nodules than in other organs. The activation of expression was first examined in leaves and roots, followed by shoot apexes. GmNMHC5 expression levels rose sharply when the plants were treated under short-day conditions (SD) and started to pod, whereas low levels were maintained in non-podding plants under long-day conditions (LD). Furthermore, overexpression of GmNMHC5 in transgenic soybean significantly promoted lateral root development and nodule building. Moreover, GmNMHC5 is upregulated by exogenous sucrose. These results indicate that GmNMHC5 can sense the sucrose signal and plays significant roles in lateral root development and nodule building. PMID:26404246

  14. Selection of alkalotolerant and symbiotically efficient chickpea nodulating rhizobia from North-West Indo Gangetic Plains.

    PubMed

    Singh, Raghvendra Pratap; Manchanda, Geetanjali; Singh, Ram Nageena; Srivastava, Alok Kumar; Dubey, R C

    2016-01-01

    In an effort to obtain reliable, alkali-tolerant, and symbiotically efficient rhizobial strains, 54 indigenous rhizobial isolates were obtained from root nodules of chickpea grown in alkaline soil of 5 different agricultural locations in North-West Indo Gangetic Plains (NW-IGP). Of these, 16 most symbiotically effective isolates were selected for polyphasic analysis (pH stress, salt tolerance, and genetic characterization). All the selected isolates were able to tolerate the high alkaline pH. Among them, CPN1, CPN8, and CPN32 grew well at pH 11.0. High pH-induced proteins were explored by SDS-PAGE assay. Identification and genetic characterization of isolates was done by 16S rRNA gene sequencing, RNA polymerase subunit-B (rpoB) and symbiotic genes (nodC and nifH). The study revealed diverse symbiotically efficient alkalotolerant chickpea nodulating rhizobial strains from NW-IGP. This study has thus contributed a valuable genetic pool of isolates that can potentially be used to increase chickpea production in these soil types. PMID:26377641

  15. Legume NADPH Oxidases Have Crucial Roles at Different Stages of Nodulation

    PubMed Central

    Montiel, Jesús; Arthikala, Manoj-Kumar; Cárdenas, Luis; Quinto, Carmen

    2016-01-01

    Plant NADPH oxidases, formerly known as respiratory burst oxidase homologues (RBOHs), are plasma membrane enzymes dedicated to reactive oxygen species (ROS) production. These oxidases are implicated in a wide variety of processes, ranging from tissue and organ growth and development to signaling pathways in response to abiotic and biotic stimuli. Research on the roles of RBOHs in the plant’s response to biotic stresses has mainly focused on plant-pathogen interactions; nonetheless, recent findings have shown that these oxidases are also involved in the legume-rhizobia symbiosis. The legume-rhizobia symbiosis leads to the formation of the root nodule, where rhizobia reduce atmospheric nitrogen to ammonia. A complex signaling and developmental pathway in the legume root hair and root facilitate rhizobial entrance and nodule organogenesis, respectively. Interestingly, several reports demonstrate that RBOH-mediated ROS production displays versatile roles at different stages of nodulation. The evidence collected to date indicates that ROS act as signaling molecules that regulate rhizobial invasion and also function in nodule senescence. This review summarizes discoveries that support the key and versatile roles of various RBOH members in the legume-rhizobia symbiosis. PMID:27213330

  16. Legume NADPH Oxidases Have Crucial Roles at Different Stages of Nodulation.

    PubMed

    Montiel, Jesús; Arthikala, Manoj-Kumar; Cárdenas, Luis; Quinto, Carmen

    2016-01-01

    Plant NADPH oxidases, formerly known as respiratory burst oxidase homologues (RBOHs), are plasma membrane enzymes dedicated to reactive oxygen species (ROS) production. These oxidases are implicated in a wide variety of processes, ranging from tissue and organ growth and development to signaling pathways in response to abiotic and biotic stimuli. Research on the roles of RBOHs in the plant's response to biotic stresses has mainly focused on plant-pathogen interactions; nonetheless, recent findings have shown that these oxidases are also involved in the legume-rhizobia symbiosis. The legume-rhizobia symbiosis leads to the formation of the root nodule, where rhizobia reduce atmospheric nitrogen to ammonia. A complex signaling and developmental pathway in the legume root hair and root facilitate rhizobial entrance and nodule organogenesis, respectively. Interestingly, several reports demonstrate that RBOH-mediated ROS production displays versatile roles at different stages of nodulation. The evidence collected to date indicates that ROS act as signaling molecules that regulate rhizobial invasion and also function in nodule senescence. This review summarizes discoveries that support the key and versatile roles of various RBOH members in the legume-rhizobia symbiosis. PMID:27213330

  17. Regulatory Patterns of a Large Family of Defensin-Like Genes Expressed in Nodules of Medicago truncatula

    PubMed Central

    Nallu, Sumitha; Silverstein, Kevin A. T.; Samac, Deborah A.; Bucciarelli, Bruna; Vance, Carroll P.; VandenBosch, Kathryn A.

    2013-01-01

    Root nodules are the symbiotic organ of legumes that house nitrogen-fixing bacteria. Many genes are specifically induced in nodules during the interactions between the host plant and symbiotic rhizobia. Information regarding the regulation of expression for most of these genes is lacking. One of the largest gene families expressed in the nodules of the model legume Medicago truncatula is the nodule cysteine-rich (NCR) group of defensin-like (DEFL) genes. We used a custom Affymetrix microarray to catalog the expression changes of 566 NCRs at different stages of nodule development. Additionally, bacterial mutants were used to understand the importance of the rhizobial partners in induction of NCRs. Expression of early NCRs was detected during the initial infection of rhizobia in nodules and expression continued as nodules became mature. Late NCRs were induced concomitantly with bacteroid development in the nodules. The induction of early and late NCRs was correlated with the number and morphology of rhizobia in the nodule. Conserved 41 to 50 bp motifs identified in the upstream 1,000 bp promoter regions of NCRs were required for promoter activity. These cis-element motifs were found to be unique to the NCR family among all annotated genes in the M. truncatula genome, although they contain sub-regions with clear similarity to known regulatory motifs involved in nodule-specific expression and temporal gene regulation. PMID:23573247

  18. Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci.

    PubMed

    Beukes, Chrizelle W; Stępkowski, Tomasz; Venter, Stephanus N; Cłapa, Tomasz; Phalane, Francina L; le Roux, Marianne M; Steenkamp, Emma T

    2016-07-01

    The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic analysis of the genes responsible for their symbiotic abilities (i.e., those encoded on the nodulation [nod] and nitrogen-fixation [nif] loci) has facilitated the development of an extensive phylogeographic framework for the genus. This framework however contains only a few nodulating isolates from Africa. Here we focused on nodulating Bradyrhizobium isolates associated with native southern African legumes in the tribes Genisteae and Crotalarieae found along the Great Escarpment in the Mpumalanga Province of South Africa. The aims of this study were to: (1) obtain rhizobial isolates from legumes in the Genisteae and Crotalarieae; (2) verify their nodulation ability; (3) characterize them to species level based on phylogenetic analyses of several protein coding gene regions (atpD, dnaK, glnII, recA, rpoB and gyrB) and (4) determine their placement in the phylogeographic framework inferred from the sequences of the symbiotic loci nodA and nifD. Twenty of the 21 Bradyrhizobium isolates belonged to six novel species, while one was conspecific with the recently described B. arachidis. Among these isolates, the nodA phylogeny revealed several new clades, with 18 of our isolates found in Clades XIV and XV, and only three forming part of the cosmopolitan Clade III. These strains formed predominantly the same groups in the nifD phylogeny although with slight differences; indicating that both vertical and horizontal inheritance of the symbiotic loci occurred. These findings suggest that the largely unexplored diversity of indigenous African rhizobia are characterized by unique ancestries that might mirror the distribution of their hosts and the environmental factors driving their evolution. PMID:27068839

  19. Gamma proteobacteria can nodulate legumes of the genus Hedysarum.

    PubMed

    Benhizia, Yacine; Benhizia, Hayet; Benguedouar, Ammar; Muresu, Rosella; Giacomini, Alessio; Squartini, Andrea

    2004-08-01

    The bacteria hosted in the root nodules of the three Mediterranean wild legume species Hedysarum carnosum, Hedysarum spinosissimum subsp. capitatum, and Hedysarum pallidum, growing in native stands in different habitats in Algeria were isolated. Bacteria were recovered on yeast-mannitol-agar or on minimal media from a total of 52 nodules. Isolates were analyzed by Amplified Ribosomal DNA Restriction Analysis (ARDRA) using the enzyme CfoI, and further sorted by RAPD fingerprinting. A total of ten different types were found and their amplified 16S rDNA was sequenced and compared to databases. The BLAST alignment indicates that all the species whose sequences share 98 to 100% identity to the bacteria found in these nodules belong to the class Gammaproteobacteria and include Pantoea agglomerans, Enterobacter kobei, Enterobacter cloacae, Leclercia adecarboxylata, Escherichia vulneris, and Pseudomonas sp. No evidence of any rhizobial-like sequence was found even upon amplifying from the bulk of microbial cells obtained from the squashed nodules, suggesting that the exclusive occupants of the nodules formed by the three plants tested are members of the orders Enterobacteriales or Pseudomonadales. This is the first report of Gammaproteobacteria associated with legume nodules. Despite the presence of the related crop plant Hedysarum coronarium, specifically nodulated by Rhizobium sullae, these three Hedysarum species demonstrate to have undergone a separate path in terms of endophytic interactions with bacteria. An hypothesis to account for differences between the symbiotic relationships engaged by man-managed legumes, and those found in plants whose ecology is independent from human action, is discussed. PMID:15368852

  20. Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus

    PubMed Central

    Kalloniati, Chrysanthi; Krompas, Panagiotis; Udvardi, Michael K.; Flemetakis, Emmanouil

    2015-01-01

    We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix+) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5′-phosphosulfate reductase activity and strong 35S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix− mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation. PMID:26296963

  1. Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus.

    PubMed

    Kalloniati, Chrysanthi; Krompas, Panagiotis; Karalias, Georgios; Udvardi, Michael K; Rennenberg, Heinz; Herschbach, Cornelia; Flemetakis, Emmanouil

    2015-09-01

    We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix(+)) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5'-phosphosulfate reductase activity and strong (35)S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix(-) mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation. PMID:26296963

  2. Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts.

    PubMed

    Bontemps, Cyril; Rogel, Marco Antonio; Wiechmann, Anja; Mussabekova, Assel; Moody, Sarah; Simon, Marcelo F; Moulin, Lionel; Elliott, Geoffrey N; Lacercat-Didier, Laurence; Dasilva, Cindy; Grether, Rosaura; Camargo-Ricalde, Sara L; Chen, Weimin; Sprent, Janet I; Martínez-Romero, Esperanza; Young, J Peter W; James, Euan K

    2016-01-01

    The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species. We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for betaproteobacteria using in situ immunolocalization. Rhizobia isolated from the nodules were genetically characterized and tested for their ability to nodulate Mimosa spp. Immunological analysis of 25 host taxa suggested that most (including all the highland endemics) were not nodulated by betaproteobacteria. Phylogenetic analyses of 16S rRNA, recA, nodA, nodC and nifH genes from 87 strains isolated from 20 taxa confirmed that the endemic Mexican Mimosa species favoured alphaproteobacteria in the genera Rhizobium and Ensifer: this was confirmed by nodulation tests. Host phylogeny, geographic isolation and coevolution with symbionts derived from very different soils have potentially contributed to the striking difference in the choice of symbiotic partners by Mexican and Brazilian Mimosa species. PMID:26214613

  3. Mixed Nodule Infection in Sinorhizobium meliloti–Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior

    PubMed Central

    Checcucci, Alice; Azzarello, Elisa; Bazzicalupo, Marco; Galardini, Marco; Lagomarsino, Alessandra; Mancuso, Stefano; Marti, Lucia; Marzano, Maria C.; Mocali, Stefano; Squartini, Andrea; Zanardo, Marina; Mengoni, Alessio

    2016-01-01

    In the symbiosis between rhizobia and legumes, host plants can form symbiotic root nodules with multiple rhizobial strains, potentially showing different symbiotic performances in nitrogen fixation. Here, we investigated the presence of mixed nodules, containing rhizobia with different degrees of mutualisms, and evaluate their relative fitness in the Sinorhizobium meliloti–Medicago sativa model symbiosis. We used three S. meliloti strains, the mutualist strains Rm1021 and BL225C and the non-mutualist AK83. We performed competition experiments involving both in vitro and in vivo symbiotic assays with M. sativa host plants. We show the occurrence of a high number (from 27 to 100%) of mixed nodules with no negative effect on both nitrogen fixation and plant growth. The estimation of the relative fitness as non-mutualist/mutualist ratios in single nodules shows that in some nodules the non-mutualist strain efficiently colonized root nodules along with the mutualist ones. In conclusion, we can support the hypothesis that in S. meliloti–M. sativa symbiosis mixed nodules are formed and allow non-mutualist or less-mutualist bacterial partners to be less or not sanctioned by the host plant, hence allowing a potential form of cheating behavior to be present in the nitrogen fixing symbiosis. PMID:27379128

  4. Mixed Nodule Infection in Sinorhizobium meliloti-Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior.

    PubMed

    Checcucci, Alice; Azzarello, Elisa; Bazzicalupo, Marco; Galardini, Marco; Lagomarsino, Alessandra; Mancuso, Stefano; Marti, Lucia; Marzano, Maria C; Mocali, Stefano; Squartini, Andrea; Zanardo, Marina; Mengoni, Alessio

    2016-01-01

    In the symbiosis between rhizobia and legumes, host plants can form symbiotic root nodules with multiple rhizobial strains, potentially showing different symbiotic performances in nitrogen fixation. Here, we investigated the presence of mixed nodules, containing rhizobia with different degrees of mutualisms, and evaluate their relative fitness in the Sinorhizobium meliloti-Medicago sativa model symbiosis. We used three S. meliloti strains, the mutualist strains Rm1021 and BL225C and the non-mutualist AK83. We performed competition experiments involving both in vitro and in vivo symbiotic assays with M. sativa host plants. We show the occurrence of a high number (from 27 to 100%) of mixed nodules with no negative effect on both nitrogen fixation and plant growth. The estimation of the relative fitness as non-mutualist/mutualist ratios in single nodules shows that in some nodules the non-mutualist strain efficiently colonized root nodules along with the mutualist ones. In conclusion, we can support the hypothesis that in S. meliloti-M. sativa symbiosis mixed nodules are formed and allow non-mutualist or less-mutualist bacterial partners to be less or not sanctioned by the host plant, hence allowing a potential form of cheating behavior to be present in the nitrogen fixing symbiosis. PMID:27379128

  5. The independent acquisition of plant root nitrogen-fixing symbiosis in Fabids recruited the same genetic pathway for nodule organogenesis.

    PubMed

    Svistoonoff, Sergio; Benabdoun, Faiza Meriem; Nambiar-Veetil, Mathish; Imanishi, Leandro; Vaissayre, Virginie; Cesari, Stella; Diagne, Nathalie; Hocher, Valérie; de Billy, Françoise; Bonneau, Jocelyne; Wall, Luis; Ykhlef, Nadia; Rosenberg, Charles; Bogusz, Didier; Franche, Claudine; Gherbi, Hassen

    2013-01-01

    Only species belonging to the Fabid clade, limited to four classes and ten families of Angiosperms, are able to form nitrogen-fixing root nodule symbioses (RNS) with soil bacteria. This concerns plants of the legume family (Fabaceae) and Parasponia (Cannabaceae) associated with the Gram-negative proteobacteria collectively called rhizobia and actinorhizal plants associated with the Gram-positive actinomycetes of the genus Frankia. Calcium and calmodulin-dependent protein kinase (CCaMK) is a key component of the common signaling pathway leading to both rhizobial and arbuscular mycorrhizal symbioses (AM) and plays a central role in cross-signaling between root nodule organogenesis and infection processes. Here, we show that CCaMK is also needed for successful actinorhiza formation and interaction with AM fungi in the actinorhizal tree Casuarina glauca and is also able to restore both nodulation and AM symbioses in a Medicago truncatula ccamk mutant. Besides, we expressed auto-active CgCCaMK lacking the auto-inhibitory/CaM domain in two actinorhizal species: C. glauca (Casuarinaceae), which develops an intracellular infection pathway, and Discaria trinervis (Rhamnaceae) which is characterized by an ancestral intercellular infection mechanism. In both species, we found induction of nodulation independent of Frankia similar to response to the activation of CCaMK in the rhizobia-legume symbiosis and conclude that the regulation of actinorhiza organogenesis is conserved regardless of the infection mode. It has been suggested that rhizobial and actinorhizal symbioses originated from a common ancestor with several independent evolutionary origins. Our findings are consistent with the recruitment of a similar genetic pathway governing rhizobial and Frankia nodule organogenesis. PMID:23741336

  6. The Independent Acquisition of Plant Root Nitrogen-Fixing Symbiosis in Fabids Recruited the Same Genetic Pathway for Nodule Organogenesis

    PubMed Central

    Svistoonoff, Sergio; Benabdoun, Faiza Meriem; Nambiar-Veetil, Mathish; Imanishi, Leandro; Vaissayre, Virginie; Cesari, Stella; Diagne, Nathalie; Hocher, Valérie; de Billy, Françoise; Bonneau, Jocelyne; Wall, Luis; Ykhlef, Nadia; Rosenberg, Charles; Bogusz, Didier; Franche, Claudine; Gherbi, Hassen

    2013-01-01

    Only species belonging to the Fabid clade, limited to four classes and ten families of Angiosperms, are able to form nitrogen-fixing root nodule symbioses (RNS) with soil bacteria. This concerns plants of the legume family (Fabaceae) and Parasponia (Cannabaceae) associated with the Gram-negative proteobacteria collectively called rhizobia and actinorhizal plants associated with the Gram-positive actinomycetes of the genus Frankia. Calcium and calmodulin-dependent protein kinase (CCaMK) is a key component of the common signaling pathway leading to both rhizobial and arbuscular mycorrhizal symbioses (AM) and plays a central role in cross-signaling between root nodule organogenesis and infection processes. Here, we show that CCaMK is also needed for successful actinorhiza formation and interaction with AM fungi in the actinorhizal tree Casuarina glauca and is also able to restore both nodulation and AM symbioses in a Medicago truncatula ccamk mutant. Besides, we expressed auto-active CgCCaMK lacking the auto-inhibitory/CaM domain in two actinorhizal species: C. glauca (Casuarinaceae), which develops an intracellular infection pathway, and Discaria trinervis (Rhamnaceae) which is characterized by an ancestral intercellular infection mechanism. In both species, we found induction of nodulation independent of Frankia similar to response to the activation of CCaMK in the rhizobia-legume symbiosis and conclude that the regulation of actinorhiza organogenesis is conserved regardless of the infection mode. It has been suggested that rhizobial and actinorhizal symbioses originated from a common ancestor with several independent evolutionary origins. Our findings are consistent with the recruitment of a similar genetic pathway governing rhizobial and Frankia nodule organogenesis. PMID:23741336

  7. Genetic Variability in Nodulation and Root Growth Affects Nitrogen Fixation and Accumulation in Pea

    PubMed Central

    Bourion, Virginie; Laguerre, Gisele; Depret, Geraldine; Voisin, Anne-Sophie; Salon, Christophe; Duc, Gerard

    2007-01-01

    Background and Aims Legume nitrogen is derived from two different sources, symbiotically fixed atmospheric N2 and soil N. The effect of genetic variability of root and nodule establishment on N acquisition and seed protein yield was investigated under field conditions in pea (Pisum sativum). In addition, these parameters were related to the variability in preference for rhizobial genotypes. Methods Five different spring pea lines (two hypernodulating mutants and three cultivars), previously identified in artificial conditions as contrasted for both root and nodule development, were characterized under field conditions. Root and nodule establishment was examined from the four-leaf stage up to the beginning of seed filling and was related to the patterns of shoot dry matter and nitrogen accumulation. The genetic structure of rhizobial populations associated with the pea lines was obtained by analysis of nodule samples. The fraction of nitrogen derived from symbiotic fixation was estimated at the beginning of seed filling and at physiological maturity, when seed protein content and yield were determined. Key Results The hypernodulating mutants established nodules earlier and maintained them longer than was the case for the three cultivars, whereas their root development and nitrogen accumulation were lower. The seed protein yield was higher in ‘Athos’ and ‘Austin’, the two cultivars with increased root development, consistent with their higher N absorption during seed filling. Conclusion The hypernodulating mutants did not accumulate more nitrogen, probably due to the C cost for nodulation being higher than for root development. Enhancing exogenous nitrogen supply at the end of the growth cycle, by increasing the potential for root N uptake from soil, seems a good option for improving pea seed filling. PMID:17670753

  8. Nodulation in Dimorphandra wilsonii Rizz. (Caesalpinioideae), a Threatened Species Native to the Brazilian Cerrado

    PubMed Central

    Fonseca, Márcia Bacelar; Peix, Alvaro; de Faria, Sergio Miana; Mateos, Pedro F.; Rivera, Lina P.; Simões-Araujo, Jean L.; França, Marcel Giovanni Costa; dos Santos Isaias, Rosy Mary; Cruz, Cristina; Velázquez, Encarna; Scotti, Maria Rita; Sprent, Janet I.; James, Euan K.

    2012-01-01

    The threatened caesalpinioid legume Dimorphandra wilsonii, which is native to the Cerrado biome in Brazil, was examined for its nodulation and N2-fixing ability, and was compared with another, less-threatened species, D. jorgei. Nodulation and potential N2 fixation was shown on seedlings that had been inoculated singly with five bradyrhizobial isolates from mature D. wilsonii nodules. The infection of D. wilsonii by two of these strains (Dw10.1, Dw12.5) was followed in detail using light and transmission electron microscopy, and was compared with that of D. jorgei by Bradyrhizobium strain SEMIA6099. The roots of D. wilsonii were infected via small transient root hairs at 42 d after inoculation (dai), and nodules were sufficiently mature at 63 dai to express nitrogenase protein. Similar infection and nodule developmental processes were observed in D. jorgei. The bacteroids in mature Dimorphandra nodules were enclosed in plant cell wall material containing a homogalacturonan (pectic) epitope that was recognized by the monoclonal antibody JIM5. Analysis of sequences of their rrs (16S rRNA) genes and their ITS regions showed that the five D. wilsonii strains, although related to SEMIA6099, may constitute five undescribed species of genus Bradyrhizobium, whilst their nodD and nifH gene sequences showed that they formed clearly separated branches from other rhizobial strains. This is the first study to describe in full the N2-fixing symbiotic interaction between defined rhizobial strains and legumes in the sub-family Caesalpinioideae. This information will hopefully assist in the conservation of the threatened species D. wilsonii. PMID:23185349

  9. Solitary pulmonary nodule

    MedlinePlus

    ... doctor must decide whether the nodule in your lung is most likely benign (not cancer) or of concern. A nodule more likely benign if: The nodule is small, has a smooth border, and has a solid and even appearance on an x-ray or CT scan You are young and do ...

  10. Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS.

    PubMed

    Ziegler, Dominik; Pothier, Joël F; Ardley, Julie; Fossou, Romain Kouakou; Pflüger, Valentin; de Meyer, Sofie; Vogel, Guido; Tonolla, Mauro; Howieson, John; Reeve, Wayne; Perret, Xavier

    2015-07-01

    Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS. PMID:25776061

  11. [Thyroid nodules – how to proceed?].

    PubMed

    Murer, Karin; Müller, Werner

    2016-01-01

    Asymptomatic thyroid nodules are very common and detected with increasing frequency by radiological investigations of the neck as so-called “incidentalomas”. If a thyroid nodule is found, the question arises how to proceed with this case. The goal is to recognize the very rare malignant nodules and to perform an adequate therapy. Every work-up of a thyroid nodule includes functional evaluation by determination of thyroid stimulating hormone (TSH). Is the level of the hormone suppressed, a scintigraphy is indicated to rule out a hot thyroid nodule implying a benign finding. Ultrasound is the imaging of choice for the thyroid gland and provides information with respect to size, number and configuration of the nodes. Depending on sonographic evaluation and other possible risk factors, a fine-needle aspiration biopsy of the node is performed. Based on the cytologic findings further therapeutic procedures are determined. PMID:27132640

  12. Characteristics of Woodland Rhizobial Populations from Surface- and Deep-Soil Environments of the Sonoran Desert

    PubMed Central

    Waldon, Hollis B.; Jenkins, Michael B.; Virginia, Ross A.; Harding, Ethelynda E.

    1989-01-01

    A collection of 74 rhizobial isolates recovered from nodules of the desert woody legumes Prosopis glandulosa, Psorothamnus spinosus, and Acacia constricta were characterized by using 61 nutritional and biochemical tests. We compared isolates from A. constricta and Prosopis glandulosa and tested the hypothesis that the rhizobia from a deep-phreatic rooting zone of a Prosopis woodland in the Sonoran Desert of southern California were phenetically distinct from rhizobia from surface soils. Cluster analysis identified four major homogeneous groups. The first phenon contained slow-growing (SG) Prosopis rhizobia from surface and deep-phreatic-soil environments. These isolates grew poorly on most of the media used in the study, probably because of their requirement for a high medium pH. The second group of isolates primarily contained SG Prosopis rhizobia from the deep-phreatic rooting environment and included two fast-growing (FG) Psorothamnus rhizobia. These isolates were nutritionally versatile and grew over a broad pH range. The third major phenon was composed mainly of FG Prosopis rhizobia from surface and dry subsurface soils. While these isolates used a restricted range of carbohydrates (including sucrose) as sole carbon sources, they showed better growth on a range of organic acids as sole carbon sources and amino acids as sole carbon and nitrogen sources than did other isolates in the study. They grew better at 36°C than at 26°C. The FG Acacia rhizobia from surface-soil environments formed a final major phenon that was distinct from the Prosopis isolates. They produced very high absorbance readings on all of the carbohydrates tested except sucrose, grew poorly on many of the other substrates tested, and preferred a 36 to a 26°C incubation temperature. The surface populations of Prosopis rhizobia required a higher pH for growth and, under the conditions used in this study, were less tolerant of low solute potential and high growth temperature than were phreatic

  13. Diversity of endophytic bacteria associated with nodules of two indigenous legumes at different altitudes of the Qilian Mountains in China.

    PubMed

    Xu, Lin; Zhang, Yong; Wang, Li; Chen, Weimin; Wei, Gehong

    2014-09-01

    A total of 201 endophytic root nodule-associated bacteria collected from two legumes indigenous to different Qilian Mountain altitudes (Hexi Corridor) were characterized through 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, 16S rRNA gene sequence analysis, and enterobacterial repetitive intergenic consensus-PCR clustering. The isolates phylogenetically belonged to 35 species in the Phyllobacterium, Ensifer, Rhizobium, Microvirga, Sphingomonas, Paracoccus, Mycobacterium, Paenibacillus, Cohnella, Sporosarcina, Bacillus, Staphylococcus, Brevibacterium, Xenophilus, Erwinia, Leclercia, Acinetobacter, and Pseudomonas genera. Phylogenetic nodA sequence analysis showed higher similarity to Sinorhizobium meliloti with strains related to the Rhizobium, Sinorhizobium, and Acinetobacter genera. Sequence analysis of the nifH gene revealed that the strains belonging to Xenophilus, Acinetobacter, Phyllobacterium, and Rhizobium had genes similar to those of Mesorhizobium and Sinorhizobium. The results indicated that horizontal gene transfer could have occurred between rhizobia and non-rhizobial endophytes. Canonical correspondence analysis revealed that altitude and host plant species contributed more to the bacterial endosymbiont separation than other ecological factors. This study provided valuable information on the interactions between symbiotic bacteria, non-symbiotic bacteria and their habitats, and thus provided knowledge on their genetic diversity and ecology. PMID:24985194

  14. Variation of Clonal, Mesquite-Associated Rhizobial and Bradyrhizobial Populations from Surface and Deep Soils by Symbiotic Gene Region Restriction Fragment Length Polymorphism and Plasmid Profile Analysis

    PubMed Central

    Thomas, P. M.; Golly, K. F.; Zyskind, J. W.; Virginia, R. A.

    1994-01-01

    Genetic characteristics of 14 Rhizobium and 9 Bradyrhizobium mesquite (Prosopis glandulosa)-nodulating strains isolated from surface (0- to 0.5-m) and deep (4- to 6-m) rooting zones were determined in order to examine the hypothesis that surface- and deep-soil symbiont populations were related but had become genetically distinct during adaptation to contrasting soil conditions. To examine genetic diversity, Southern blots of PstI-digested genomic DNA were sequentially hybridized with the nodDABC region of Rhizobium meliloti, the Klebsiella pneumoniae nifHDK region encoding nitrogenase structural genes, and the chromosome-localized ndvB region of R. meliloti. Plasmid profile and host plant nodulation assays were also made. Isolates from mesquite nodulated beans and cowpeas but not alfalfa, clover, or soybeans. Mesquite was nodulated by diverse species of symbionts (R. meliloti, Rhizobium leguminosarum bv. phaseoli, and Parasponia bradyrhizobia). There were no differences within the groups of mesquite-associated rhizobia or bradyrhizobia in cross-inoculation response. The ndvB hybridization results showed the greatest genetic diversity among rhizobial strains. The pattern of ndvB-hybridizing fragments suggested that surface and deep strains were clonally related, but groups of related strains from each soil depth could be distinguished. Less variation was found with nifHDK and nodDABC probes. Large plasmids (>1,500 kb) were observed in all rhizobia and some bradyrhizobia. Profiles of plasmids of less than 1,000 kb were related to the soil depth and the genus of the symbiont. We suggest that interacting selection pressures for symbiotic competence and free-living survival, coupled with soil conditions that restrict genetic exchange between surface and deep-soil populations, led to the observed patterns of genetic diversity. Images PMID:16349226

  15. Variation of clonal, mesquite-associated rhizobial and bradyrhizobial populations from surface and deep soils by symbiotic gene region restriction fragment length polymorphism and plasmid profile analysis.

    PubMed

    Thomas, P M; Golly, K F; Zyskind, J W; Virginia, R A

    1994-04-01

    Genetic characteristics of 14 Rhizobium and 9 Bradyrhizobium mesquite (Prosopis glandulosa)-nodulating strains isolated from surface (0- to 0.5-m) and deep (4- to 6-m) rooting zones were determined in order to examine the hypothesis that surface- and deep-soil symbiont populations were related but had become genetically distinct during adaptation to contrasting soil conditions. To examine genetic diversity, Southern blots of PstI-digested genomic DNA were sequentially hybridized with the nodDABC region of Rhizobium meliloti, the Klebsiella pneumoniae nifHDK region encoding nitrogenase structural genes, and the chromosome-localized ndvB region of R. meliloti. Plasmid profile and host plant nodulation assays were also made. Isolates from mesquite nodulated beans and cowpeas but not alfalfa, clover, or soybeans. Mesquite was nodulated by diverse species of symbionts (R. meliloti, Rhizobium leguminosarum bv. phaseoli, and Parasponia bradyrhizobia). There were no differences within the groups of mesquite-associated rhizobia or bradyrhizobia in cross-inoculation response. The ndvB hybridization results showed the greatest genetic diversity among rhizobial strains. The pattern of ndvB-hybridizing fragments suggested that surface and deep strains were clonally related, but groups of related strains from each soil depth could be distinguished. Less variation was found with nifHDK and nodDABC probes. Large plasmids (>1,500 kb) were observed in all rhizobia and some bradyrhizobia. Profiles of plasmids of less than 1,000 kb were related to the soil depth and the genus of the symbiont. We suggest that interacting selection pressures for symbiotic competence and free-living survival, coupled with soil conditions that restrict genetic exchange between surface and deep-soil populations, led to the observed patterns of genetic diversity. PMID:16349226

  16. Gatekeeper Tyrosine Phosphorylation of SYMRK Is Essential for Synchronizing the Epidermal and Cortical Responses in Root Nodule Symbiosis.

    PubMed

    Saha, Sudip; Paul, Anindita; Herring, Laura; Dutta, Ayan; Bhattacharya, Avisek; Samaddar, Sandip; Goshe, Michael B; DasGupta, Maitrayee

    2016-05-01

    Symbiosis receptor kinase (SYMRK) is indispensable for activation of root nodule symbiosis (RNS) at both epidermal and cortical levels and is functionally conserved in legumes. Previously, we reported SYMRK to be phosphorylated on "gatekeeper" Tyr both in vitro as well as in planta. Since gatekeeper phosphorylation was not necessary for activity, the significance remained elusive. Herein, we show that substituting gatekeeper with nonphosphorylatable residues like Phe or Ala significantly affected autophosphorylation on selected targets on activation segment/αEF and β3-αC loop of SYMRK. In addition, the same gatekeeper mutants failed to restore proper symbiotic features in a symrk null mutant where rhizobial invasion of the epidermis and nodule organogenesis was unaffected but rhizobia remain restricted to the epidermis in infection threads migrating parallel to the longitudinal axis of the root, resulting in extensive infection patches at the nodule apex. Thus, gatekeeper phosphorylation is critical for synchronizing epidermal/cortical responses in RNS. PMID:26960732

  17. Different Pathways Act Downstream of the CEP Peptide Receptor CRA2 to Regulate Lateral Root and Nodule Development.

    PubMed

    Mohd-Radzman, Nadiatul A; Laffont, Carole; Ivanovici, Ariel; Patel, Neha; Reid, Dugald; Stougaard, Jens; Frugier, Florian; Imin, Nijat; Djordjevic, Michael A

    2016-08-01

    C-TERMINALLY ENCODED PEPTIDEs (CEPs) control root system architecture in a non-cell-autonomous manner. In Medicago truncatula, MtCEP1 affects root development by increasing nodule formation and inhibiting lateral root emergence by unknown pathways. Here, we show that the MtCEP1 peptide-dependent increase in nodulation requires the symbiotic signaling pathway and ETHYLENE INSENSITIVE2 (EIN2)/SICKLE (SKL), but acts independently of SUPER NUMERIC NODULES. MtCEP1-dependent inhibition of lateral root development acts through an EIN2-independent mechanism. MtCEP1 increases nodulation by promoting rhizobial infections, the developmental competency of roots for nodulation, the formation of fused nodules, and an increase in frequency of nodule development that initiates at proto-phloem poles. These phenotypes are similar to those of the ein2/skl mutant and support that MtCEP1 modulates EIN2-dependent symbiotic responses. Accordingly, MtCEP1 counteracts the reduction in nodulation induced by increasing ethylene precursor concentrations, and an ethylene synthesis inhibitor treatment antagonizes MtCEP1 root phenotypes. MtCEP1 also inhibits the development of EIN2-dependent pseudonodule formation. Finally, mutants affecting the COMPACT ROOT ARCHITECTURE2 (CRA2) receptor, which is closely related to the Arabidopsis CEP Receptor1, are unresponsive to MtCEP1 effects on lateral root and nodule formation, suggesting that CRA2 is a CEP peptide receptor mediating both organogenesis programs. In addition, an ethylene inhibitor treatment counteracts the cra2 nodulation phenotype. These results indicate that MtCEP1 and its likely receptor, CRA2, mediate nodulation and lateral root development through different pathways. PMID:27342310

  18. Different Pathways Act Downstream of the CEP Peptide Receptor CRA2 to Regulate Lateral Root and Nodule Development1[OPEN

    PubMed Central

    Mohd-Radzman, Nadiatul A.; Ivanovici, Ariel; Frugier, Florian; Djordjevic, Michael A.

    2016-01-01

    C-TERMINALLY ENCODED PEPTIDEs (CEPs) control root system architecture in a non-cell-autonomous manner. In Medicago truncatula, MtCEP1 affects root development by increasing nodule formation and inhibiting lateral root emergence by unknown pathways. Here, we show that the MtCEP1 peptide-dependent increase in nodulation requires the symbiotic signaling pathway and ETHYLENE INSENSITIVE2 (EIN2)/SICKLE (SKL), but acts independently of SUPER NUMERIC NODULES. MtCEP1-dependent inhibition of lateral root development acts through an EIN2-independent mechanism. MtCEP1 increases nodulation by promoting rhizobial infections, the developmental competency of roots for nodulation, the formation of fused nodules, and an increase in frequency of nodule development that initiates at proto-phloem poles. These phenotypes are similar to those of the ein2/skl mutant and support that MtCEP1 modulates EIN2-dependent symbiotic responses. Accordingly, MtCEP1 counteracts the reduction in nodulation induced by increasing ethylene precursor concentrations, and an ethylene synthesis inhibitor treatment antagonizes MtCEP1 root phenotypes. MtCEP1 also inhibits the development of EIN2-dependent pseudonodule formation. Finally, mutants affecting the COMPACT ROOT ARCHITECTURE2 (CRA2) receptor, which is closely related to the Arabidopsis CEP Receptor1, are unresponsive to MtCEP1 effects on lateral root and nodule formation, suggesting that CRA2 is a CEP peptide receptor mediating both organogenesis programs. In addition, an ethylene inhibitor treatment counteracts the cra2 nodulation phenotype. These results indicate that MtCEP1 and its likely receptor, CRA2, mediate nodulation and lateral root development through different pathways. PMID:27342310

  19. Penile Epithelioid Angiomatoid Nodule.

    PubMed

    Pirpiris, Athina; Gilbourd, Daniel; Ranasinghe, Anudini; Dill, Tony; Lynnhtun, Kyaw; Rindani, Rahul

    2015-10-01

    Cutaneous epithelioid angiomatoid nodule is a rare clinical entity that is common on the trunk and limbs. This is the first report of penile cutaneous epithelioid angiomatoid nodule. Although it is a benign entity, it must be differentiated from vascular neoplasms, as it can bear similar clinical and pathologic features. PMID:26171823

  20. Effect of Co-Inoculation with Mycorrhiza and Rhizobia on the Nodule Trehalose Content of Different Bean Genotypes

    PubMed Central

    Ballesteros-Almanza, L; Altamirano-Hernandez, J; Peña-Cabriales, J.J; Santoyo, G; Sanchez-Yañez, J.M; Valencia-Cantero, E; Macias-Rodriguez, L; Lopez-Bucio, J; Cardenas-Navarro, R; Farias-Rodriguez, R

    2010-01-01

    Studies on Rhizobium-legume symbiosis show that trehalose content in nodules under drought stress correlates positively with an increase in plant tolerance to this stress. Fewer reports describe trehalose accumulation in mycorrhiza where, in contrast with rhizobia, there is no flux of carbohydrates from the microsymbiont to the plant. However, the trehalose dynamics in the Mycorrhiza-Rhizobium-Legume tripartite symbiosis is unknown. The present study explores the role of this tripartite symbiosis in the trehalose content of nodules grown under contrasting moisture conditions. Three wild genotypes (P. filiformis, P. acutifolis and P. vulgaris) and two commercial genotypes of Phaseolus vulgaris (Pinto villa and Flor de Mayo) were used. Co-inoculation treatments were conducted with Glomus intraradices and a mixture of seven native rhizobial strains, and trehalose content was determined by GC/MS. The results showed a negative effect of mycorrhizal inoculation on nodule development, as mycorrhized plants showed fewer nodules and lower nodule dry weight compared to plants inoculated only with Rhizobium. Mycorrhizal colonization was also higher in plants inoculated only with Glomus as compared to plants co-inoculated with both microsymbionts. In regard to trehalose, co-inoculation negatively affects its accumulation in the nodules of each genotype tested. However, the correlation analysis showed a significantly positive correlation between mycorrhizal colonization and nodule trehalose content. PMID:21253462

  1. [Pulmonary nodules and arachnophobia].

    PubMed

    Colinet, B; Dargent, J-L; Fremault, A

    2014-01-01

    Pulmonary nodules are a common reason for consultation and their investigation must always exclude a possible neoplastic cause. This means that, in addition to a thorough history, investigations may be necessary which are sometimes invasive and therefore potentially a cause of iatrogenic harm. The toxic aetiologies for pulmonary nodules are rare. We report a case of a patient with pulmonary nodules occurring predominantly in the right lung, about 1cm in diameter, non-cavitating without calcification, and sometimes surrounded by a peripheral halo. The nodules were a chance finding during preoperative evaluation. After a comprehensive review, a reaction to an inhaled irritant was the preferred hypothesis, specifically overuse of a compound insecticide containing, in addition to the propellant gas and solvent type hydrocarbon - a mixture of piperonyl butoxide, of esbiothrine and permethrin. Removal of this led to the complete disappearance of nodules. Pathological examination identified bronchiolitis obliterans with organising pneumonia accompanied by non-necrotizing granulomas and lipid vacuoles. PMID:24461445

  2. Proof that Burkholderia Strains Form Effective Symbioses with Legumes: a Study of Novel Mimosa-Nodulating Strains from South America

    PubMed Central

    Chen, Wen-Ming; de Faria, Sergio M.; Straliotto, Rosângela; Pitard, Rosa M.; Simões-Araùjo, Jean L.; Chou, Jui-Hsing; Chou, Yi-Ju; Barrios, Edmundo; Prescott, Alan R.; Elliott, Geoffrey N.; Sprent, Janet I.; Young, J. Peter W.; James, Euan K.

    2005-01-01

    Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes. PMID:16269788

  3. Phenotypic and genomic characteristics of rhizobia isolated from Genista tinctoria root nodules.

    PubMed

    Kalita, Michał; Małek, Wanda

    2004-11-01

    Forty three rhizobial strains isolated from root nodules of Genista tinctoria growing in England, Ukraine, and Poland were compared with 21 representatives of the recognized rhizobial species and two unclassified Bradyrhizobium sp. (Lupinus) strains by performing a numerical analysis of 102 phenotypic features and with the reference bradyrhizobia by simplified AFLP analysis with one restriction enzyme PstI and one selective primer PstI-A. All Genista tinctoria microsymbionts were slow-growing bradyrhizobia with generation time of 10-14 h, acid tolerant, salt sensitive, and antibiotic resistant. Cluster analysis based on the phenotypic properties of all bacteria included, grouped dyer's broom rhizobia together with Bradyrhizobium strains, and classified them into three major phena according to their geographic origin. Genista tinctoria nodule isolates were separated into three clusters with the strain composition as in a phenogrouping by AFLP patterns. The presented results, suggest the relationship of G. tincoria microsymbionts to Bradyrhizobium species and show the usefulness of AFLP analysis for differentiation and classification of the studied rhizobia. PMID:15612629

  4. [Analysis of Symbiotic Genes of Leguminous Plants Nodule Bacteria Grown in the Southern Urals].

    PubMed

    Baymiev, An Kh; Ivanova, E S; Gumenko, R S; Chubukova, O V; Baymiev, Al Kh

    2015-12-01

    Bacterial strains isolated from the nodules, tissues, and root surface of wild legumes growing in the Southern Urals related to the tribes Galegeae, Hedysareae, Genisteae, Trifolieae, and Loteae were examined for the presence in their genomes of symbiotic (sym) genes. It was found that the sym-genes are present in microorganisms isolated only from the nodules of the analyzed plants (sym+ -strains). Phylogenetic analysis of sym+ -strains on the basis of a comparative analysis of 16S rRNA gene sequences showed that sym+ -strains belong to five families of nodule bacteria: Mesorhizobium, Bradyrhizobium, Sinorhizobium, Rhizobium, and Phyllobacterium. A study the phylogeny of the sym-genes showed that the nodule bacteria of leguminous plants of the Southern Urals at the genus level are mainly characterized by a parallel evolution of symbiotic genes and the 16S rRNA gene. Thus, cases of horizontal transfer of sym genes, which sometimes leads to the formation of certain types of atypical rhizobial strains ofleguminous plants, are detected in nodule bacteria populations. PMID:27055295

  5. Root nodule bacteria from Clitoria ternatea L. are putative invasive nonrhizobial endophytes.

    PubMed

    Aeron, Abhinav; Chauhan, Puneet Singh; Dubey, Ramesh Chand; Maheshwari, Dinesh Kumar; Bajpai, Vivek K

    2015-02-01

    In this study, bacteria (8 species and 5 genera) belonging to the classes Betaproteobacteria, Gammaproteobacteria, and Sphingobacteria were isolated from root nodules of the multipurpose legume Clitoria ternatea L. and identified on the basis of partial 16S rRNA sequencing. The root nodule bacteria were subjected to phenotypic clustering and diversity studies using biochemical kits, including Hi-Media Carbokit™, Enterobacteriaceae™ identification kit, ERIC-PCR, and 16S ARDRA. All the strains showed growth on Ashby's N-free media over 7 generations, indicative of presumptive nitrogen fixation and further confirmed by amplification of the nifH gene. None of the strains showed the capability to renodulate the host plant, neither alone nor in combination with standard rhizobial strains, which was further confirmed by the absence of nodC bands in PCR assay. The results clearly indicate the common existence of nonrhizobial microflora inside the root nodules of legumes, which were thought to be colonized only by rhizobia and were responsible for N2 fixation in leguminous crops. However, with the recent discovery of nodule endophytes from a variety of legumes, as also observed here, it can be assumed that symbiotic rhizobia are not all alone and that these invasive endophytes belonging to various bacterial genera are more than just opportunistic colonizers of specialized nodule niche. PMID:25619106

  6. Influence of tree canopy on N₂ fixation by pasture legumes and soil rhizobial abundance in Mediterranean oak woodlands.

    PubMed

    Carranca, C; Castro, I V; Figueiredo, N; Redondo, R; Rodrigues, A R F; Saraiva, I; Maricato, R; Madeira, M A V

    2015-02-15

    Symbiotic N2 fixation is of primordial significance in sustainable agro-forestry management as it allows reducing the use of mineral N in the production of mixed stands and by protecting the soils from degradation. Thereby, on a 2-year basis, N2 fixation was evaluated in four oak woodlands under Mediterranean conditions using a split-plot design and three replicates. (15)N technique was used for determination of N2 fixation rate. Variations in environmental conditions (temperature, rainfall, radiation) by the cork tree canopy as well as the age of stands and pasture management can cause great differences in vegetation growth, legume N2 fixation, and soil rhizobial abundance. In the present study, non-legumes dominated the swards, in particular beneath the tree canopy, and legumes represented only 42% of total herbage. A 2-fold biomass reduction was observed in the oldest sown pasture in relation to the medium-age sward (6 t DW ha(-1)yr(-1)). Overall, competition of pasture growth for light was negligible, but soil rhizobial abundance and symbiotic N2 fixation capacity were highly favored by this environmental factor in the spring and outside the influence of tree canopy. Nitrogen derived from the atmosphere was moderate to high (54-72%) in unsown and sown swards. Inputs of fixed N2 increased from winter to spring due to more favorable climatic conditions (temperature and light intensity) for both rhizobia and vegetation growths. Assuming a constant fixation rate at each seasonal period, N2 fixation capacity increased from about 0.10 kg N ha(-1) per day in the autumn-winter period to 0.15 kg N ha(-1) per day in spring. Belowground plant material contributed to 11% of accumulated N in pasture legumes and was not affected by canopy. Size of soil fixing bacteria contributed little to explain pasture legumes N. PMID:25460942

  7. Rhizobial characterization in revegetated areas after bauxite mining.

    PubMed

    Borges, Wardsson Lustrino; Prin, Yves; Ducousso, Marc; Le Roux, Christine; de Faria, Sergio Miana

    2016-01-01

    Little is known regarding how the increased diversity of nitrogen-fixing bacteria contributes to the productivity and diversity of plants in complex communities. However, some authors have shown that the presence of a diverse group of nodulating bacteria is required for different plant species to coexist. A better understanding of the plant symbiotic organism diversity role in natural ecosystems can be extremely useful to define recovery strategies of environments that were degraded by human activities. This study used ARDRA, BOX-PCR fingerprinting and sequencing of the 16S rDNA gene to assess the diversity of root nodule nitrogen-fixing bacteria in former bauxite mining areas that were replanted in 1981, 1985, 1993, 1998, 2004 and 2006 and in a native forest. Among the 12 isolates for which the 16S rDNA gene was partially sequenced, eight, three and one isolate(s) presented similarity with sequences of the genera Bradyrhizobium, Rhizobium and Mesorhizobium, respectively. The richness, Shannon and evenness indices were the highest in the area that was replanted the earliest (1981) and the lowest in the area that was replanted most recently (2006). PMID:26991294

  8. Characterization of the papilionoid-Burkholderia interaction in the Fynbos biome: The diversity and distribution of beta-rhizobia nodulating Podalyria calyptrata (Fabaceae, Podalyrieae).

    PubMed

    Lemaire, Benny; Van Cauwenberghe, Jannick; Verstraete, Brecht; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Sprent, Janet; James, Euan K; Muasya, A Muthama

    2016-02-01

    The South African Fynbos soils are renowned for nitrogen-fixing Burkholderia associated with diverse papilionoid legumes of the tribes Crotalarieae, Hypocalypteae, Indigofereae, Phaseoleae and Podalyrieae. However, despite numerous rhizobial studies in the region, the symbiotic diversity of Burkholderia has not been investigated in relation to a specific host legume and its geographical provenance. This study analyzed the diversity of nodulating strains of Burkholderia from the legume species Podalyria calyptrata. Diverse lineages were detected that proved to be closely related to Burkholderia taxa, originating from hosts in other legume tribes. By analyzing the genetic variation of chromosomal (recA) and nodulation (nodA) sequence data in relation to the sampling sites we assessed the geographical distribution patterns of the P. calyptrata symbionts. Although we found a degree of genetically differentiated rhizobial populations, a correlation between genetic (recA and nodA) and geographic distances among populations was not observed, suggesting high rates of dispersal and rhizobial colonization within Fynbos soils. PMID:26689612

  9. Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

    PubMed Central

    Sánchez, Maximo; Ramírez-Bahena, Martha-Helena; Peix, Alvaro; Lorite, María J.; Sanjuán, Juan; Monza, Jorge

    2014-01-01

    Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium. The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium, for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T). PMID:24271211

  10. [Therapy of thyroid nodules].

    PubMed

    Schott, Matthias

    2015-04-01

    Thyroid nodules are frequent in Germany. In about every fourth person thyroid nodules can be detected. Most of them are benign. Signs for malignancy are hypoechogenicity, microcalcifications, an unregular margin and increased blood perfusion. There is no strict indication for the treatment of benign nodules. In most cases iodine supplementation is sufficient. A combination therapy with levothyroxine and iodine is more efficient for the treatment of larger nodules. Subclinical hyperthyroidism caused by an adenoma does not necessarily need to be treated, whereas manifest hyperthyroidism needs to treated in most cases with antithyroid drug therapy. Radioiodine therapy is the classical indication for the treatment of unifocal autonomous adenomas. A largely increased thyroid gland with and without uni- / multifocal adenomas are often operated. PMID:25831118

  11. Occurrence of nodulation in unexplored leguminous trees native to the West African tropical rainforest and inoculation response of native species useful in reforestation.

    PubMed

    Diabate, Moussa; Munive, Antonio; de Faria, Sérgio Miana; Ba, Amadou; Dreyfus, Bernard; Galiana, Antoine

    2005-04-01

    Despite the abundance and diversity of timber tree legumes in the West African rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. In the first part of this study the occurrence of nodulation was determined in 156 leguminous species growing in six natural forest areas in Guinea, mostly mature trees. In the second part, an in situ experiment of rhizobial inoculation was performed on eight selected tree species belonging to three genera: Albizia, Erythrophleum and Millettia. Of the 97 plant species and 14 genera that had never been examined before this study, 31 species and four genera were reported to be nodulated. After 4 months of growing in a nursery and a further 11 months after transplantation of plants to the field, we observed a highly significant (P < 0.001) and positive effect of inoculation with Bradyrhizobium sp. strains on the growth of the eight tree species tested. The importance of determining the nodulation ability of unexplored local trees and subsequently using this information for inoculation in reforestation programmes was demonstrated. PMID:15760366

  12. Abundance and diversity of soybean-nodulating rhizobia in black soil are impacted by land use and crop management.

    PubMed

    Yan, Jun; Han, Xiao Zeng; Ji, Zhao Jun; Li, Yan; Wang, En Tao; Xie, Zhi Hong; Chen, Wen Feng

    2014-09-01

    To investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) were distributed widely in all treatments, while Bradyrhizobium sp. II was found only in GL treatment. Cultivation with soybeans increased the rhizobial abundance and diversity, except for the soybean monoculture (S-S) treatment. In monoculture systems, soybeans favored Bradyrhizobium sp. I, while maize and wheat favored Bradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes but did not change the species composition. The organic carbon (OC) and available phosphorus (AP) contents and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I and II and Bradyrhizobium japonicum and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land uses and crop management could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and legume or nonlegume plants, which offered novel information about the biogeography of rhizobia. PMID:24951780

  13. Abundance and Diversity of Soybean-Nodulating Rhizobia in Black Soil Are Impacted by Land Use and Crop Management

    PubMed Central

    Yan, Jun; Ji, Zhao Jun; Li, Yan; Wang, En Tao; Xie, Zhi Hong

    2014-01-01

    To investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) were distributed widely in all treatments, while Bradyrhizobium sp. II was found only in GL treatment. Cultivation with soybeans increased the rhizobial abundance and diversity, except for the soybean monoculture (S-S) treatment. In monoculture systems, soybeans favored Bradyrhizobium sp. I, while maize and wheat favored Bradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes but did not change the species composition. The organic carbon (OC) and available phosphorus (AP) contents and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I and II and Bradyrhizobium japonicum and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land uses and crop management could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and legume or nonlegume plants, which offered novel information about the biogeography of rhizobia. PMID:24951780

  14. Expression of the CLE-RS3 gene suppresses root nodulation in Lotus japonicus.

    PubMed

    Nishida, Hanna; Handa, Yoshihiro; Tanaka, Sachiko; Suzaki, Takuya; Kawaguchi, Masayoshi

    2016-09-01

    Cell-to-cell communication, principally mediated by short- or long-range mobile signals, is involved in many plant developmental processes. In root nodule symbiosis, a mutual relationship between leguminous plants and nitrogen-fixing rhizobia, the mechanism for the autoregulation of nodulation (AON) plays a key role in preventing the production of an excess number of nodules. AON is based on long-distance cell-to-cell communication between roots and shoots. In Lotus japonicus, two CLAVATA3/ESR-related (CLE) peptides, encoded by CLE-ROOT SIGNAL 1 (CLE-RS1) and -RS2, act as putative root-derived signals that transmit signals inhibiting further nodule development through interaction with a shoot-acting receptor-like kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1). Here, an in silico search and subsequent expression analyses enabled us to identify two new L. japonicus CLE genes that are potentially involved in nodulation, designated as CLE-RS3 and LjCLE40. Time-course expression patterns showed that CLE-RS1/2/3 and LjCLE40 expression is induced during nodulation with different activation patterns. Furthermore, constitutive expression of CLE-RS3 significantly suppressed nodule formation in a HAR1-dependent manner. TOO MUCH LOVE, a root-acting regulator of AON, is also required for the CLE-RS3 action. These results suggest that CLE-RS3 is a new component of AON in L. japonicus that may act as a potential root-derived signal through interaction with HAR1. Because CLE-RS2, CLE-RS3 and LjCLE40 are located in tandem in the genome and their expression is induced not only by rhizobial infection but also by nitrate, these genes may have duplicated from a common gene. PMID:27294965

  15. Chitinase-resistant hydrophilic symbiotic factors secreted by Frankia activate both Ca(2+) spiking and NIN gene expression in the actinorhizal plant Casuarina glauca.

    PubMed

    Chabaud, Mireille; Gherbi, Hassen; Pirolles, Elodie; Vaissayre, Virginie; Fournier, Joëlle; Moukouanga, Daniel; Franche, Claudine; Bogusz, Didier; Tisa, Louis S; Barker, David G; Svistoonoff, Sergio

    2016-01-01

    Although it is now well-established that decorated lipo-chitooligosaccharide Nod factors are the key rhizobial signals which initiate infection/nodulation in host legume species, the identity of the equivalent microbial signaling molecules in the Frankia/actinorhizal association remains elusive. With the objective of identifying Frankia symbiotic factors we present a novel approach based on both molecular and cellular pre-infection reporters expressed in the model actinorhizal species Casuarina glauca. By introducing the nuclear-localized cameleon Nup-YC2.1 into Casuarina glauca we show that cell-free culture supernatants of the compatible Frankia CcI3 strain are able to elicit sustained high frequency Ca(2+) spiking in host root hairs. Furthermore, an excellent correlation exists between the triggering of nuclear Ca(2+) spiking and the transcriptional activation of the ProCgNIN:GFP reporter as a function of the Frankia strain tested. These two pre-infection symbiotic responses have been used in combination to show that the signal molecules present in the Frankia CcI3 supernatant are hydrophilic, of low molecular weight and resistant to chitinase degradation. In conclusion, the biologically active symbiotic signals secreted by Frankia appear to be chemically distinct from the currently known chitin-based rhizobial/arbuscular mycorrhizal signaling molecules. Convenient bioassays in Casuarina glauca are now available for their full characterization. PMID:26484850

  16. A transcriptomic analysis of the effect of genistein on Sinorhizobium fredii HH103 reveals novel rhizobial genes putatively involved in symbiosis.

    PubMed

    Pérez-Montaño, F; Jiménez-Guerrero, I; Acosta-Jurado, S; Navarro-Gómez, P; Ollero, F J; Ruiz-Sainz, J E; López-Baena, F J; Vinardell, J M

    2016-01-01

    Sinorhizobium fredii HH103 is a rhizobial soybean symbiont that exhibits an extremely broad host-range. Flavonoids exuded by legume roots induce the expression of rhizobial symbiotic genes and activate the bacterial protein NodD, which binds to regulatory DNA sequences called nod boxes (NB). NB drive the expression of genes involved in the production of molecular signals (Nod factors) as well as the transcription of ttsI, whose encoded product binds to tts boxes (TB), inducing the secretion of proteins (effectors) through the type 3 secretion system (T3SS). In this work, a S. fredii HH103 global gene expression analysis in the presence of the flavonoid genistein was carried out, revealing a complex regulatory network. Three groups of genes differentially expressed were identified: i) genes controlled by NB, ii) genes regulated by TB, and iii) genes not preceded by a NB or a TB. Interestingly, we have found differentially expressed genes not previously studied in rhizobia, being some of them not related to Nod factors or the T3SS. Future characterization of these putative symbiotic-related genes could shed light on the understanding of the complex molecular dialogue established between rhizobia and legumes. PMID:27539649

  17. A transcriptomic analysis of the effect of genistein on Sinorhizobium fredii HH103 reveals novel rhizobial genes putatively involved in symbiosis

    PubMed Central

    Pérez-Montaño, F.; Jiménez-Guerrero, I.; Acosta-Jurado, S.; Navarro-Gómez, P.; Ollero, F. J.; Ruiz-Sainz, J. E.; López-Baena, F. J.; Vinardell, J. M.

    2016-01-01

    Sinorhizobium fredii HH103 is a rhizobial soybean symbiont that exhibits an extremely broad host-range. Flavonoids exuded by legume roots induce the expression of rhizobial symbiotic genes and activate the bacterial protein NodD, which binds to regulatory DNA sequences called nod boxes (NB). NB drive the expression of genes involved in the production of molecular signals (Nod factors) as well as the transcription of ttsI, whose encoded product binds to tts boxes (TB), inducing the secretion of proteins (effectors) through the type 3 secretion system (T3SS). In this work, a S. fredii HH103 global gene expression analysis in the presence of the flavonoid genistein was carried out, revealing a complex regulatory network. Three groups of genes differentially expressed were identified: i) genes controlled by NB, ii) genes regulated by TB, and iii) genes not preceded by a NB or a TB. Interestingly, we have found differentially expressed genes not previously studied in rhizobia, being some of them not related to Nod factors or the T3SS. Future characterization of these putative symbiotic-related genes could shed light on the understanding of the complex molecular dialogue established between rhizobia and legumes. PMID:27539649

  18. A bioinformatics insight to rhizobial globins: gene identification and mapping, polypeptide sequence and phenetic analysis, and protein modeling.

    PubMed Central

    Gesto-Borroto, Reinier; Sánchez-Sánchez, Miriam; Arredondo-Peter, Raúl

    2015-01-01

    Globins (Glbs) are proteins widely distributed in organisms. Three evolutionary families have been identified in Glbs: the M, S and T Glb families. The M Glbs include flavohemoglobins (fHbs) and single-domain Glbs (SDgbs); the S Glbs include globin-coupled sensors (GCSs), protoglobins and sensor single domain globins, and the T Glbs include truncated Glbs (tHbs). Structurally, the M and S Glbs exhibit 3/3-folding whereas the T Glbs exhibit 2/2-folding. Glbs are widespread in bacteria, including several rhizobial genomes. However, only few rhizobial Glbs have been characterized. Hence, we characterized Glbs from 62 rhizobial genomes using bioinformatics methods such as data mining in databases, sequence alignment, phenogram construction and protein modeling. Also, we analyzed soluble extracts from Bradyrhizobium japonicum USDA38 and USDA58 by (reduced + carbon monoxide (CO) minus reduced) differential spectroscopy. Database searching showed that only fhb, sdgb, gcs and thb genes exist in the rhizobia analyzed in this work. Promoter analysis revealed that apparently several rhizobial glb genes are not regulated by a -10 promoter but might be regulated by -35 and Fnr (fumarate-nitrate reduction regulator)-like promoters. Mapping analysis revealed that rhizobial fhbs and thbs are flanked by a variety of genes whereas several rhizobial sdgbs and gcss are flanked by genes coding for proteins involved in the metabolism of nitrates and nitrites and chemotaxis, respectively. Phenetic analysis showed that rhizobial Glbs segregate into the M, S and T Glb families, while structural analysis showed that predicted rhizobial SDgbs and fHbs and GCSs globin domain and tHbs fold into the 3/3- and 2/2-folding, respectively. Spectra from B. japonicum USDA38 and USDA58 soluble extracts exhibited peaks and troughs characteristic of bacterial and vertebrate Glbs thus indicating that putative Glbs are synthesized in B. japonicum USDA38 and USDA58. PMID:26594329

  19. Nodulating Competitiveness of a Nonmotile Tn7 Mutant of Bradyrhizobium japonicum in Nonsterile Soil †

    PubMed Central

    Liu, Ruilong; Tran, Van Mai; Schmidt, E. L.

    1989-01-01

    A nonmotile mutant of Bradyrhizobium japonicum serogroup 127 was generated by Tn7 mutagenesis and matched with the wild type against a common competitor in studies of soybean nodulation in nonsterile soil. The Tn7 mutant was very similar to the wild type in growth rate in culture, soybean lectin-binding ability, flagellar morphology, and nodulating capability, but it had a longer lag phase. Competing strains were distributed uniformly in soil in various ratios and at different population densities prior to planting. Mutant and wild type were equally prevalent in the seedling rhizosphere at about the time of nodule initiation, suggesting that motility conferred no advantage in rhizosphere colonization. Nodulation success of the Tn7 mutant was lower than that of the wild type under all test conditions. Differences were greatest at low soil populations of competitors and much less pronounced at initial populations of 107 g−1. The longer lag phase of the Tn7 mutant may have contributed to its decreased competitiveness, especially at the higher inoculation levels. The antibiotic and motility markers were stable, and the rifampin resistance derived from the parent did not affect adversely the competitiveness of the Tn7 mutant. We found motility to be of limited importance to the competitiveness of a strain in normal nonsterile soil, where the significance, if any, of this ability may be in migration at the immediate root surface in soils sparsely populated with rhizobial symbionts. PMID:16347986

  20. Modulation of endogenous indole-3-acetic acid biosynthesis in bacteroids within Medicago sativa nodules.

    PubMed

    Bianco, C; Senatore, B; Arbucci, S; Pieraccini, G; Defez, R

    2014-07-01

    To evaluate the dose-response effects of endogenous indole-3-acetic acid (IAA) on Medicago plant growth and dry weight production, we increased the synthesis of IAA in both free-living and symbiosis-stage rhizobial bacteroids during Rhizobium-legume symbiosis. For this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of iaaM and tms2 genes for IAA biosynthesis. A positive correlation was found between the higher expression of IAA biosynthetic genes in free-living bacteria and the increased production of IAA under both free-living and symbiotic conditions. Plants nodulated by RD65 and RD66 strains, synthetizing the highest IAA concentration, showed a significant (up to 73%) increase in the shoot fresh weight and upregulation of nitrogenase gene, nifH, compared to plants nodulated by the wild-type strain. When these plants were analyzed by confocal microscopy, using an anti-IAA antibody, the strongest signal was observed in bacteroids of Medicago sativa RD66 (Ms-RD66) plants, even when they were located in the senescent nodule zone. We show here a simple system to modulate endogenous IAA biosynthesis in bacteria nodulating legumes suitable to investigate which is the maximum level of IAA biosynthesis, resulting in the maximal increase of plant growth. PMID:24814784

  1. Diversity of Rhizobia Nodulating Phaseolus vulgaris L. in Two Kenyan Soils with Contrasting pHs

    PubMed Central

    Anyango, B.; Wilson, K. J.; Beynon, J. L.; Giller, K. E.

    1995-01-01

    Rhizobia were isolated from two Kenyan soils with pHs of 4.5 and 6.8 and characterized on the basis of their host ranges for nodulation and nitrogen fixation, colony morphologies, restriction fragment fingerprints, and hybridization with a nifH probe. The populations of rhizobia nodulating Phaseolus vulgaris in the two soils were similar in numbers and in effectiveness of N(inf2) fixation but were markedly different in composition. The population in the Naivasha soil (pH 6.8) was dominated by isolates specific in host range for nodulation to P. vulgaris; these all had multiple copies, in most cases four, of the structural nitrogenase gene nifH. Only one of the isolates from this soil formed effective nodules on Leucaena leucocephala, and this isolate had only a single copy of nifH. By contrast, the population in the acid Daka-ini soil (pH 4.5) was composed largely of broad-host-range isolates which had single copies of nifH. The isolates from the Daka-ini soil which were specific to P. vulgaris generally had three copies of nifH, although one isolate had only two copies. These rhizobial isolates are indigenous to Kenyan soils and yet have marked similarities to previously described Rhizobium species from other continents. PMID:16535165

  2. Remodeling of the Infection Chamber before Infection Thread Formation Reveals a Two-Step Mechanism for Rhizobial Entry into the Host Legume Root Hair1

    PubMed Central

    Teillet, Alice; Chabaud, Mireille; Ivanov, Sergey; Genre, Andrea; Limpens, Erik; de Carvalho-Niebel, Fernanda; Barker, David G.

    2015-01-01

    In many legumes, root entry of symbiotic nitrogen-fixing rhizobia occurs via host-constructed tubular tip-growing structures known as infection threads (ITs). Here, we have used a confocal microscopy live-tissue imaging approach to investigate early stages of IT formation in Medicago truncatula root hairs (RHs) expressing fluorescent protein fusion reporters. This has revealed that ITs only initiate 10 to 20 h after the completion of RH curling, by which time major modifications have occurred within the so-called infection chamber, the site of bacterial entrapment. These include the accumulation of exocytosis (M. truncatula Vesicle-Associated Membrane Protein721e)- and cell wall (M. truncatula EARLY NODULIN11)-associated markers, concomitant with radial expansion of the chamber. Significantly, the infection-defective M. truncatula nodule inception-1 mutant is unable to create a functional infection chamber. This underlines the importance of the NIN-dependent phase of host cell wall remodeling that accompanies bacterial proliferation and precedes IT formation, and leads us to propose a two-step model for rhizobial infection initiation in legume RHs. PMID:25659382

  3. OxyR-regulated catalase activity is critical for oxidative stress resistance, nodulation and nitrogen fixation in Azorhizobium caulinodans.

    PubMed

    Zhao, Yue; Nickels, Logan M; Wang, Hui; Ling, Jun; Zhong, Zengtao; Zhu, Jun

    2016-07-01

    The legume-rhizobial interaction results in the formation of symbiotic nodules in which rhizobia fix nitrogen. During the process of symbiosis, reactive oxygen species (ROS) are generated. Thus, the response of rhizobia to ROS is important for successful nodulation and nitrogen fixation. In this study, we investigated how Azorhizobium caulinodans, a rhizobium that forms both root and stem nodules on its host plant, regulates ROS resistance. We found that in-frame deletions of a gene encoding the putative catalase-peroxidase katG or a gene encoding a LysR-family regulatory protein, oxyR, exhibited increased sensitivity to H2O2 We then showed that OxyR positively regulated katG expression in an H2O2-independent fashion. Furthermore, we found that deletion of katG or oxyR led to significant reduction in the number of stem nodules and decrease of nitrogen fixation capacities in symbiosis. Our results revealed that KatG and OxyR are not only critical for antioxidant defense in vitro, but also important for nodule formation and nitrogen fixation during interaction with plant hosts. PMID:27190162

  4. Solitary liver nodules.

    PubMed

    Fisher, A W; Curry, B; Jacques, J

    1975-05-17

    There has been confusion in the literature over the nomenclature of solitary liver nodules. Several such lesions have recently been reported in patients taking oral contraceptives. Similarities exist between these cases that suggest they may be examples of focal nodular hyperplasia. Here three further cases are presented. The criteria for making the diagnosis and its importance are discussed. PMID:165001

  5. Solitary pulmonary nodule

    MedlinePlus

    ... chest x-ray Pulmonary nodule, solitary - CT scan Respiratory system References Gotway MB, Panse PM, Gruden JF, Elicker BM. Thoracic radiology. In: Broaddus VC, Mason RJ, Ernst JD, et al, eds. Murray and Nadel's Textbook of Respiratory Medicine . 6th ed. Philadelphia, PA: Elsevier Saunders; 2016: ...

  6. Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

    PubMed Central

    Tian, Chang Fu; Zhou, Yuan Jie; Zhang, Yan Ming; Li, Qin Qin; Zhang, Yun Zeng; Li, Dong Fang; Wang, Shuang; Wang, Jun; Gilbert, Luz B.; Li, Ying Rui; Chen, Wen Xin

    2012-01-01

    The rhizobium–legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium–legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process. PMID:22586130

  7. Evidence based imaging strategies for solitary pulmonary nodule

    PubMed Central

    Gong, Jing-Shan; Suzuki, Kenji; Morcos, Sameh K.

    2014-01-01

    Solitary pulmonary nodule (SPN) is defined as a rounded opacity ≤3 cm in diameter surrounded by lung parenchyma. The majority of smokers who undergo thin-section CT have SPNs, most of which are smaller than 7 mm. In the past, multiple follow-up examinations over a two-year period, including CT follow-up at 3, 6, 12, 18, and 24 months, were recommended when such nodules are detected incidentally. This policy increases radiation burden for the affected population. Nodule features such as shape, edge characteristics, cavitation, and location have not yet been found to be accurate for distinguishing benign from malignant nodules. When SPN is considered to be indeterminate in the initial exam, the risk factor of the patients should be evaluated, which includes patients’ age and smoking history. The 2005 Fleischner Society guideline stated that at least 99% of all nodules 4 mm or smaller are benign; when nodule is 5-9 mm in diameter, the best strategy is surveillance. The timing of these control examinations varies according to the nodule size (4-6, or 6-8 mm) and the type of patients, specifically at low or high risk of malignancy concerned. Noncalcified nodules larger than 8 mm diameter bear a substantial risk of malignancy, additional options such as contrast material-enhanced CT, positron emission tomography (PET), percutaneous needle biopsy, and thoracoscopic resection or videoassisted thoracoscopic resection should be considered. PMID:25093083

  8. Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471

    PubMed Central

    Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; Tiwari, Ravi; Howieson, John; Yates, Ronald; O’Hara, Graham; Ninawi, Mohamed; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

    2013-01-01

    Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976882

  9. Biochemical and ultrasonographic parameters influencing thyroid nodules elasticity.

    PubMed

    Szczepanek-Parulska, Ewelina; Woliński, Kosma; Stangierski, Adam; Gurgul, Edyta; Ruchała, Marek

    2014-11-01

    Elastography is a method of tissue stiffness assessment. It has already been demonstrated that thyroid cancers are less elastic than benign lesions. However, little is known about other factors, which might influence the stiffness of thyroid nodules and disrupt the prediction of malignancy using this technique. The aim of this study was to conduct the first systematic assessment of factors potentially affecting the elasticity of thyroid lesions. One hundred and twenty-two patients with thyroid nodular disease admitted for thyroidectomy underwent preoperative ultrasonography and sonoelastography. The definite diagnosis of thyroid lesions was based on histological examination. What was evaluated in the study was the influence of composition, size, localization, nodularity, and selected laboratory parameters on thyroid nodule elasticity. Firstly, association between the above-mentioned factors and elasticity was assessed in benign lesions. Secondly, all nodules (benign and malignant) were divided into subgroups according to the presence or absence of particular features, which turned out to be an important disturbing factor increasing the stiffness of the lesion in the first step of analysis. There were 22 malignant and 371 benign lesions. The analysis of benign lesions revealed that the presence calcifications (p < 0.0001) significantly increased nodule stiffness. Partially, cystic nodules were significantly less elastic than solid ones (p = 0.03). There was also positive correlation between nodule size and stiffness (p < 0.0001). Lesions localized in the isthmus were significantly less elastic than nodules in other localizations. (p = 0.0001). Solitary nodules were less elastic than lesions in multinodular goiter (p = 0.006). Correlation between Tg concentration and stiffness was significant (p < 0.0001, r = 0.24). The concentration of anti-thyroid autoantibodies was associated with stiffness at the border of significance. However, there was no significant

  10. Higher TSH can be used as an additional risk factor in prediction of malignancy in euthyroid thyroid nodules evaluated by cytology based on Bethesda system.

    PubMed

    Baser, Husniye; Topaloglu, Oya; Tam, Abbas Ali; Evranos, Berna; Alkan, Afra; Sungu, Nuran; Dumlu, Ersin Gurkan; Ersoy, Reyhan; Cakir, Bekir

    2016-08-01

    Recently, it has been suggested that thyrotropin (TSH) concentration can be used as a marker for prediction of thyroid malignancy. In this study, we aimed to investigate the association between TSH levels and prediction of malignancy in euthyroid patients with different Bethesda categories. The data of 1433 euthyroid patients with 3206 thyroid nodules who underwent thyroidectomy were screened retrospectively. The preoperative cytology results, thyroid function tests, thyroid autoantibodies, and presence of histopathological Hashimoto's thyroiditis (HT) were recorded. Of the 1433 patients, 585 (40.8 %) had malignant and 848 (59.2 %) had benign histopathology. Malignant group had smaller nodule size, elevated TSH levels, and higher rate of presence of HT compared to benign group (p < 0.001, all). Cytology results of 3206 nodules were as follows: 832 nondiagnostic (ND), 1666 benign, 392 atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS), 68 follicular neoplasm/suspicious for follicular neoplasm (FN/SFN), 133 suspicious for malignancy (SM), and 115 malignant. Both SM and malignant cytology groups had higher TSH levels than other 4 Bethesda categories (p < 0.05, all). Benign cytology group had significantly lower TSH levels compared to other cytology groups (p < 0.05, all). Patients with malignant final histopathology in ND and AUS/FLUS cytology groups had significantly higher TSH levels compared to patients with benign final histopathology (p < 0.05, all). Moreover, TSH levels showed to increase from Bethesda categories II to VI. In addition to cytology, higher TSH levels can be used as a supplementary marker in prediction of malignancy in certain Bethesda categories. PMID:26972701

  11. Noduler an immune protein augments infection-induced cell proliferation through cross-talking with p38 MAPK.

    PubMed

    Satyavathi, Valluri V; Narra, Deepa; Nagaraju, Javaregowda

    2016-02-01

    Noduler, an immune protein that mediates nodule formation by binding to specific bacteria and hemocytes was previously reported in the wild tasar silkworm, Antheraea mylitta. However, the molecular mechanism underlying nodulation in lepidopterans remains unclear. The present study is performed to investigate the functional connection between Noduler with various signalling pathways. It was observed that Noduler is an upstream factor in the phenoloxidase cascade and its knockdown has no direct effect on Toll/Imd pathway inducible genes. Additionally, Noduler was shown to stimulate cell proliferation via activation of p38 mitogen-activated protein kinase (MAPK). Inhibition of p38 in the infected hemocytes cultured in vitro resulted in reduced cell proliferation and melanization. These results suggest that Noduler mediates nodulation via p38/MAPK signalling. This is the first report implicating the p38 MAPK signalling pathway in the nodulation response of insects. PMID:26433868

  12. Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia.

    PubMed

    Fterich, A; Mahdhi, M; Caviedes, M A; Pajuelo, E; Rivas, R; Rodriguez-Llorente, I D; Mars, M

    2011-06-01

    Diversity of 50 bacterial isolates recovered from root nodules of Prosopis farcta grown in different arid soils in Tunisia, was investigated. Characterization of isolates was assessed using a polyphasic approach including phenotypic characteristics, 16S rRNA gene PCR--RFLP and sequencing, nodA gene sequencing and MLSA. It was found that most of isolates are tolerant to high temperature (40°C) and salinity (3%). Genetic characterization emphasizes that isolates were assigned to the genus Ensifer (80%), Mesorhizobium (4%) and non-nodulating endophytic bacteria (16%). Forty isolates belonging to the genus Ensifer were affiliated to Ensifer meliloti, Ensifer xinjiangense/Ensifer fredii and Ensifer numidicus species. Two isolates belonged to the genus Mesorhizobium. Eight isolates failing to renodulate their host plant were endophytic bacteria and belonged to Bacillus, Paenibacillus and Acinetobacter genera. Symbiotic properties of nodulating isolates showed a diversity in their capacity to infect their host plant and fix atmospheric nitrogen. Isolate PG29 identified as Ensifer meliloti was the most effective one. Ability of Prosopis farcta to establish symbiosis with rhizobial species confers an important advantage for this species to be used in reforestation programs. This study offered the first systematic information about the diversity of microsymbionts nodulating Prosopis farcta in the arid regions of Tunisia. PMID:21359955

  13. Interactions between ethylene, gibberellins, and brassinosteroids in the development of rhizobial and mycorrhizal symbioses of pea.

    PubMed

    Foo, Eloise; McAdam, Erin L; Weller, James L; Reid, James B

    2016-04-01

    The regulation of arbuscular mycorrhizal development and nodulation involves complex interactions between the plant and its microbial symbionts. In this study, we use the recently identified ethylene-insensitiveein2mutant in pea (Pisum sativumL.) to explore the role of ethylene in the development of these symbioses. We show that ethylene acts as a strong negative regulator of nodulation, confirming reports in other legumes. Minor changes in gibberellin1and indole-3-acetic acid levels inein2roots appear insufficient to explain the differences in nodulation. Double mutants produced by crosses betweenein2and the severely gibberellin-deficientnaand brassinosteroid-deficientlkmutants showed increased nodule numbers and reduced nodule spacing compared with thenaandlksingle mutants, but nodule numbers and spacing were typical ofein2plants, suggesting that the reduced number of nodules innaandlkplants is largely due to the elevated ethylene levels previously reported in these mutants. We show that ethylene can also negatively regulate mycorrhizae development when ethylene levels are elevated above basal levels, consistent with a role for ethylene in reducing symbiotic development under stressful conditions. In contrast to the hormone interactions in nodulation,ein2does not override the effect oflkornaon the development of arbuscular mycorrhizae, suggesting that brassinosteroids and gibberellins influence this process largely independently of ethylene. PMID:26889005

  14. Interactions between ethylene, gibberellins, and brassinosteroids in the development of rhizobial and mycorrhizal symbioses of pea

    PubMed Central

    Foo, Eloise; McAdam, Erin L.; Weller, James L.; Reid, James B.

    2016-01-01

    The regulation of arbuscular mycorrhizal development and nodulation involves complex interactions between the plant and its microbial symbionts. In this study, we use the recently identified ethylene-insensitive ein2 mutant in pea (Pisum sativum L.) to explore the role of ethylene in the development of these symbioses. We show that ethylene acts as a strong negative regulator of nodulation, confirming reports in other legumes. Minor changes in gibberellin1 and indole-3-acetic acid levels in ein2 roots appear insufficient to explain the differences in nodulation. Double mutants produced by crosses between ein2 and the severely gibberellin-deficient na and brassinosteroid-deficient lk mutants showed increased nodule numbers and reduced nodule spacing compared with the na and lk single mutants, but nodule numbers and spacing were typical of ein2 plants, suggesting that the reduced number of nodules in na and lk plants is largely due to the elevated ethylene levels previously reported in these mutants. We show that ethylene can also negatively regulate mycorrhizae development when ethylene levels are elevated above basal levels, consistent with a role for ethylene in reducing symbiotic development under stressful conditions. In contrast to the hormone interactions in nodulation, ein2 does not override the effect of lk or na on the development of arbuscular mycorrhizae, suggesting that brassinosteroids and gibberellins influence this process largely independently of ethylene. PMID:26889005

  15. Rhizobial galactoglucan determines the predatory pattern of Myxococcus xanthus and protects Sinorhizobium meliloti from predation

    PubMed Central

    Pérez, Juana; Jiménez-Zurdo, José I.; Martínez-Abarca, Francisco; Millán, Vicenta; Shimkets, Lawrence J.; Muñoz-Dorado, José

    2014-01-01

    Summary Myxococcus xanthus is a social bacterium that preys on prokaryotic and eukaryotic microorganisms. Co-culture of M. xanthus with reference laboratory strains and field isolates of the legume symbiont Sinorhizobium meliloti revealed two different predatory patterns that resemble frontal and wolfpack attacks. Use of mutants impaired in the two types of M. xanthus surface motility (A or adventurous and S or social motility) and a csgA mutant, which is unable to form macroscopic travelling waves known as ripples, has demonstrated that both motility systems but not rippling are required for efficient predation. To avoid frontal attack and reduce killing rates, rhizobial cells require a functional expR gene. ExpR regulates expression of genes involved in a variety of functions. The use of S. meliloti mutants impaired in several of these functions revealed that the exopolysaccharide galactoglucan (EPS II) is the major determinant of the M. xanthus predatory pattern. The data also suggest that this biopolymer confers an ecological advantage to rhizobial survival in soil, which may have broad environmental implications. PMID:24707988

  16. Production and Excretion of Nod Metabolites by Rhizobium leguminosarum bv. trifolii Are Disrupted by the Same Environmental Factors That Reduce Nodulation in the Field

    PubMed Central

    McKay, Ian A.; Djordjevic, Michael A.

    1993-01-01

    Lipooligosaccharides (Nod metabolites) have been shown to be essential for the successful nodulation of legumes. In strains of Rhizobium leguminosarum bv. trifolii, Nod metabolites were detected predominantly within the cell and to a lesser extent in the periplasmic space and the growth medium. The production, and in particular the excretion, of Nod metabolites was restricted by a range of environmental conditions which are associated with poor nodulation in the field. Lowering the medium pH from 7.0 to 5.0, reducing the phosphate concentration from 1 mM to 5 μM KH2PO4, and lowering the incubation temperature from 28 to 18°C affected the number and relative concentrations of the Nod metabolites made. The form and concentration of the nitrogen source affected the relative concentrations of the Nod metabolites produced and excreted. KNO3 concentrations of >10 mM did not affect cell growth rate but substantially reduced the number of Nod metabolites released. Environmental stresses differentially altered Nod metabolite production and excretion in the same strain carrying different introduced nod regions. Strain ANU845(pWLH1) produced and excreted comparatively fewer Nod metabolites at pH 5.0 and at 18°C than strain ANU845(pRI4003). The excretion but not the production of Nod metabolites by strain ANU845(pRtO32) was dependent on the presence of both nodI and nodJ. Tn5-induced nodI and nodJ mutants did not accumulate any metabolites either outside the cell or within the outer membrane or periplasmic space. Recognition that Nod metabolite accumulation is a complex system of production and excretion, with each component responding differently to changes in environmental conditions, has many consequences, both at the molecular level and in the field. The ability of different strains to produce and release Nod metabolites is likely to be a major determinant of nodule occupancy and should be considered when screening strains suitable for adverse environments. Images PMID

  17. Rhizobial and bradyrhizobial symbionts of mesquite from the Sonoran Desert: Salt tolerance, facultative halophily, and nitrate respiration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizobial symbionts from surface and phreatic absorbing root environments of a mature mesquite woodland in the Sonoran Desert of Southern California were tested for their ability to tolerate high salinity, and respire nitrate as mechanisms of free-living survival. Isolates were grown in yeast-extra...

  18. [Benign solitary thyroid nodule (BSTN)].

    PubMed

    Pencea, V; Tiron, V; Zbranca, E; Dudeanu, I; Baran, T; Dobrescu, G; Lazăr, C; Dolinescu, C; Strat, V

    1982-01-01

    Out of a series of 210 patients (193 women and 17 men) with BSTN, 62% presented an warm nodule, 25.2% a hot nodule and 11.9% a cold nodule. The highest incidence of the nodule was noticed round the age of 40-50 years. The most common site was the middle and lower area of the right thyroid lobe. The thyroid scintigram provided orientative data regarding the nature of BSTN, the treatment indication being the surgical intervention. Histopathologically, polymorphic aspects ranging from anizofollicular adenoma, adenomatous proliferations areas and hyperfunctional aspect to degenerative sclerous alterations and lymphoplasmocitary infiltrations were noticed. The current hypotheses regarding the etiopathogeny of nodule forming process are discussed. Based on some data in the literature, we consider the nodularization of the thyroid gland as a reactional zone functional desynchronization in the conditions of some great variations of the iodate intaxe. PMID:25588244

  19. Molecular characterization and identification of plant growth promoting endophytic bacteria isolated from the root nodules of pea (Pisum sativum L.).

    PubMed

    Tariq, Mohsin; Hameed, Sohail; Yasmeen, Tahira; Zahid, Mehwish; Zafar, Marriam

    2014-02-01

    Root nodule accommodates various non-nodulating bacteria at varying densities. Present study was planned to identify and characterize the non-nodulating bacteria from the pea plant. Ten fast growing bacteria were isolated from the root nodules of cultivated pea plants. These bacterial isolates were unable to nodulate pea plants in nodulation assay, which indicate the non-rhizobial nature of these bacteria. Bacterial isolates were tested in vitro for plant growth promoting properties including indole acetic acid (IAA) production, nitrogen fixation, phosphate solubilization, root colonization and biofilm formation. Six isolates were able to produce IAA at varying level from 0.86 to 16.16 μg ml(-1), with the isolate MSP9 being most efficient. Only two isolates, MSP2 and MSP10, were able to fix nitrogen. All isolates were able to solubilize inorganic phosphorus ranging from 5.57 to 11.73 μg ml(-1), except MSP4. Bacterial isolates showed considerably better potential for colonization on pea roots. Isolates MSP9 and MSP10 were most efficient in biofilm formation on polyvinyl chloride, which indicated their potential to withstand various biotic and abiotic stresses, whereas the remaining isolates showed a very poor biofilm formation ability. The most efficient plant growth promoting agents, MSP9 and MSP10, were phylogenetically identified by 16S rRNA gene sequence analysis as Ochrobactrum and Enterobacter, respectively, with 99% similarity. It is suggested the potential endophytic bacterial strains, Ochrobactrum sp. MSP9 and Enterobacter sp. MSP10, can be used as biofertilizers for various legume and non-legume crops after studying their interaction with the host crop and field evaluation. PMID:24072498

  20. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.).

    PubMed

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. PMID:27348121

  1. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.)

    PubMed Central

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. PMID:27348121

  2. Isolated Rheumatoid Nodules: A Diagnostic Dilemma

    PubMed Central

    Gale, Michael; Gilbert, Erin; Blumenthal, David

    2015-01-01

    We present a 27-year-old male with multiple nonpainful soft tissue masses over several metacarpals, bilateral elbows, the left wrist, and both knees since the age of 4. Physical exam was significant for firm, nonmobile, nodular growths over the extensor surfaces of bilateral elbows and knees and on the 2nd and 5th metacarpal phalangeal joints. Laboratory studies revealed an unremarkable rheumatoid factor, negative ANA screening and normal joint radiographs. Differential diagnosis included subcutaneous granuloma annulare (SGA), seronegative rheumatoid nodule, and calcinosis cutis. Biopsy is the only method to distinguish benign rheumatoid nodules from SGA. This case illustrates the importance of biopsy in diagnosis, an awareness of the potential complications, and the need for good follow-up. PMID:25802526

  3. Genetic diversity of a natural population of Rhizobium leguminosarum bv. viciae nodulating plants of Vicia faba in the Vesuvian area.

    PubMed

    Ventorino, Valeria; Chiurazzi, Mario; Aponte, Maria; Pepe, Olimpia; Moschetti, Giancarlo

    2007-12-01

    A total of 98 rhizobial strains, isolated during the winter of the years 2003 (35 isolates), 2004 (33 isolates), and 2005 (30 isolates) were analyzed to determine the genetic diversity of the natural population nodulating Vicia faba plants and to identify dominant genotypes. All isolates were identified as Rhizobium leguminosarum bv. viciae by biovar-specific polymerase chain reaction amplification of the nodC gene. Intraspecific DNA polymorphism was evaluated through the restriction endonucleases analysis combined with pulsed-field gel electrophoresis. Four genotypes characterized 53% of the isolates, showing a high occurrence; moreover, they were recovered over the 3 years, thus showing a lasting persistence in the soil, which could mean a high degree of saprophytic competitiveness. The richness, diversity, and dominance indexes of genotypes were calculated to monitor the evolution of the rhizobial population during the 3 years. The genetic diversity of the analyzed strains decreased along the 3 years. In fact, the biodiversity index H' decreased from 2.6 in the first and second year to 1.9 in the third year; probably, as a result of bean monocropping, specific genotypes of Rh. leguminosarum bv. viciae were naturally selected. PMID:17899266

  4. In vitro sulfotransferase activity of NodH, a nodulation protein of Rhizobium meliloti required for host-specific nodulation.

    PubMed Central

    Ehrhardt, D W; Atkinson, E M; Faull, K F; Freedberg, D I; Sutherlin, D P; Armstrong, R; Long, S R

    1995-01-01

    Early stages of nodulation involve the exchange of signals between the bacterium and the host plant. Bacterial nodulation (nod) genes are required for Rhizobium spp. to synthesize lipooligosaccharide morphogens, termed Nod factors. The common nod genes encode enzymes that synthesize the factor core structure, which is modified by host-specific gene products. Here we show direct in vitro evidence that Rhizobium meliloti NodH, a host-specific nodulation gene, catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to the terminal 6-O position of Nod factors, and we show substrate requirements for the reaction. Our results indicate that polymerization of the chitooligosaccharide backbone likely precedes sulfation and that sulfation is not absolutely dependent on the presence or the particular structure of the N-acyl modification. NodH sulfation provides a tool for the enzymatic in vitro synthesis of novel Nod factors, or putative Nod factors intermediates, with high specific activity. PMID:7592390

  5. Allograft pancreas: pale acinar nodules.

    PubMed

    Troxell, Megan L; Drachenberg, Cinthia

    2016-08-01

    Microscopic pale-staining acinar nodules were characterized in native pancreas in the 1980s under a variety of names but have been infrequently reported since. We retrospectively studied the frequency and characteristics of pale acinar nodules in allograft pancreas biopsies, as compared to a sampling of native pancreas specimens at our center. Pale acinar nodules were present in 13% (9/69) of allograft biopsies from 22% (7/32) of transplant patients, and 23% (5/22) of native pancreas surgical specimens, although more nodules per pancreas area were present in allograft needle biopsies. Acinar nodules had size of 100 to 700 μm, were periodic acid-Schiff pale, were synaptophysin negative, stained more weakly with keratin CAM 5.2 compared to surrounding parenchyma, and had a low proliferative rate. Ultrastructural evaluation revealed paucity of zymogen granules with dilated cistern-like structures. In our experience, pale acinar nodules have similar features in allograft and native pancreas specimens, yet remain of uncertain etiology and significance. PMID:27063474

  6. Benign and malignant thyroid nodules after neck irradiation

    SciTech Connect

    Fjaelling, M.T.; Tisell, L.E.; Carlsson, S.; Hansson, G.; Lundberg, L.M.; Oden, A.

    1986-09-15

    A total of 444 persons were examined for the presence of thyroid nodules on average of 43 years after having been treated with x-rays for cervical tuberculous adenitis. Of this total, 101 subjects had undergone surgery for thyroid nodules: 25 for carcinoma (6%) and 76 for benign nodules (17%). Carcinoma occurred with the same frequency in multinodular and uninodular glands. Because of the uneven age distribution in the current series, it could not be decided whether there was a higher susceptibility of the young thyroid to the induction of thyroid carcinoma or benign nodules. The dosage range for the whole series was 0.40 to 50.90 Gy (40-5090 rad). There was a positive correlation between the absorbed radiation dose and the probability of developing benign and malignant thyroid nodules, even after doses of 20 Gy or more. The risk of developing thyroid carcinoma was equal for men and women, while the female-to-male ratio for benign nodules was 2.9:1, indicating that risk factors associated with females are of less importance in irradiated than in nonirradiated populations. The median latency for carcinoma was 40 years, suggesting that the increased risk of thyroid carcinoma after irradiation remains for the rest of the patient's life.

  7. CYTOKININ OXIDASE/DEHYDROGENASE3 Maintains Cytokinin Homeostasis during Root and Nodule Development in Lotus japonicus.

    PubMed

    Reid, Dugald E; Heckmann, Anne B; Novák, Ondřej; Kelly, Simon; Stougaard, Jens

    2016-02-01

    Cytokinins are required for symbiotic nodule development in legumes, and cytokinin signaling responses occur locally in nodule primordia and in developing nodules. Here, we show that the Lotus japonicus Ckx3 cytokinin oxidase/dehydrogenase gene is induced by Nod factor during the early phase of nodule initiation. At the cellular level, pCkx3::YFP reporter-gene studies revealed that the Ckx3 promoter is active during the first cortical cell divisions of the nodule primordium and in growing nodules. Cytokinin measurements in ckx3 mutants confirmed that CKX3 activity negatively regulates root cytokinin levels. Particularly, tZ and DHZ type cytokinins in both inoculated and uninoculated roots were elevated in ckx3 mutants, suggesting that these are targets for degradation by the CKX3 cytokinin oxidase/dehydrogenase. The effect of CKX3 on the positive and negative roles of cytokinin in nodule development, infection and regulation was further clarified using ckx3 insertion mutants. Phenotypic analysis indicated that ckx3 mutants have reduced nodulation, infection thread formation and root growth. We also identify a role for cytokinin in regulating nodulation and nitrogen fixation in response to nitrate as ckx3 phenotypes are exaggerated at increased nitrate levels. Together, these findings show that cytokinin accumulation is tightly regulated during nodulation in order to balance the requirement for cell divisions with negative regulatory effects of cytokinin on infection events and root development. PMID:26644503

  8. The Sinorhizobium (Ensifer) fredii HH103 Type 3 Secretion System Suppresses Early Defense Responses to Effectively Nodulate Soybean.

    PubMed

    Jiménez-Guerrero, Irene; Pérez-Montaño, Francisco; Monreal, José Antonio; Preston, Gail M; Fones, Helen; Vioque, Blanca; Ollero, Francisco Javier; López-Baena, Francisco Javier

    2015-07-01

    Plants that interact with pathogenic bacteria in their natural environments have developed barriers to block or contain the infection. Phytopathogenic bacteria have evolved mechanisms to subvert these defenses and promote infection. Thus, the type 3 secretion system (T3SS) delivers bacterial effectors directly into the plant cells to alter host signaling and suppress defenses, providing an appropriate environment for bacterial multiplication. Some rhizobial strains possess a symbiotic T3SS that seems to be involved in the suppression of host defenses to promote nodulation and determine the host range. In this work, we show that the inactivation of the Sinorhizobium (Ensifer) fredii HH103 T3SS negatively affects soybean nodulation in the early stages of the symbiotic process, which is associated with a reduction of the expression of early nodulation genes. This symbiotic phenotype could be the consequence of the bacterial triggering of soybean defense responses associated with the production of salicylic acid (SA) and the impairment of the T3SS mutant to suppress these responses. Interestingly, the early induction of the transcription of GmMPK4, which negatively regulates SA accumulation and defense responses in soybean via WRKY33, could be associated with the differential defense responses induced by the parental and the T3SS mutant strain. PMID:25775271

  9. Medicago truncatula natural resistance-associated macrophage Protein1 is required for iron uptake by rhizobia-infected nodule cells.

    PubMed

    Tejada-Jiménez, Manuel; Castro-Rodríguez, Rosario; Kryvoruchko, Igor; Lucas, M Mercedes; Udvardi, Michael; Imperial, Juan; González-Guerrero, Manuel

    2015-05-01

    Iron is critical for symbiotic nitrogen fixation (SNF) as a key component of multiple ferroproteins involved in this biological process. In the model legume Medicago truncatula, iron is delivered by the vasculature to the infection/maturation zone (zone II) of the nodule, where it is released to the apoplast. From there, plasma membrane iron transporters move it into rhizobia-containing cells, where iron is used as the cofactor of multiple plant and rhizobial proteins (e.g. plant leghemoglobin and bacterial nitrogenase). MtNramp1 (Medtr3g088460) is the M. truncatula Natural Resistance-Associated Macrophage Protein family member, with the highest expression levels in roots and nodules. Immunolocalization studies indicate that MtNramp1 is mainly targeted to the plasma membrane. A loss-of-function nramp1 mutant exhibited reduced growth compared with the wild type under symbiotic conditions, but not when fertilized with mineral nitrogen. Nitrogenase activity was low in the mutant, whereas exogenous iron and expression of wild-type MtNramp1 in mutant nodules increased nitrogen fixation to normal levels. These data are consistent with a model in which MtNramp1 is the main transporter responsible for apoplastic iron uptake by rhizobia-infected cells in zone II. PMID:25818701

  10. Pleiotropic effect of fluoranthene on anthocyanin synthesis and nodulation of Medicago sativa is reversed by the plant flavone luteolin

    SciTech Connect

    Wetzel, A.; Parniske, M.; Werner, D.

    1995-05-01

    The symbiosis between leguminous plants and soil bacteria of the genus Rhizobium is of considerable agronominal importance. Recently it has been found, that polycyclic aromatic hydrocarbons (PAHs; e.g. anthracene, phenanthrene, fluoranthene), occurring as ubiquitous environmental contaminants can inhibit nodulation of Medicago sativa. Fluoranthene is one of the dominant PAHs found in urban particulate matter, sewage sludge or beside motorways. Several organisms have been shown to be able to metabolize and mineralize fluoranthene but the uptake of fluoranthene is limited due to low solubility of fluoranthene in water and strong adsorption to humic substances in soil. Rhizobium meliloti cannot degrade fluoranthene. Toxic effects of fluoranthene on bacterial growth have never been observed. In contrast to their rhizobial symbiotic partners, alfalfa plants grown on a solidified fluoranthene-containing medium, exhibited symptoms of toxicity. They showed a dose-responsive decrease in shoot length and, if inoculated with R. meliloti, inhibition of nodule formation. Growth retardation is accompanied by a decrease in anthocyanin pigmentation of shoots, and an atypical accumulation of anthocyanins in roots. Plant flavonoids are known to play a central role in the signal exchange of the Legume-Rhizobium symbiosis. Phenylpropane derived compounds and flavonoids have been implicated in nodule development. Since fluoranthene impairs nodulation and induces the production of anthocyanins, it is possible that these events are causally linked via phenylpropanoid metabolism. These experiments attempt to overcome the inhibitory effects of fluoranthene by exogeneous application of the flavonoid luteolin. This paper demonstrates that luteolin antagonizes the fluoranthene mediated inhibition of nodule formation and prevents the accumulation of anthocyanins in roots. 29 refs., 4 figs., 1 tab.

  11. Genetic diversity and community structure of rhizobia nodulating Sesbania cannabina in saline-alkaline soils.

    PubMed

    Li, Yan; Li, Xiangyue; Liu, Yajing; Wang, En Tao; Ren, Chenggang; Liu, Wei; Xu, Hualing; Wu, Hailong; Jiang, Nan; Li, Yunzhao; Zhang, Xiaoli; Xie, Zhihong

    2016-05-01

    Sesbania cannabina is a plant that grows naturally along the seashores in Rudong County, China (RDC) and it has been introduced into the Yellow River Delta (YRD) as a pioneer plant to improve the saline-alkaline soils. In order to investigate the diversity of S. cannabina rhizobia in these soils, a total of 198 rhizobial isolates were characterized and phylogenetic trees were constructed based on data from multilocus sequence analysis (MLSA) of the housekeeping genes recA, atpD and glnII, as well as 16S rRNA. Symbiotic features were also studied by establishing the phylogeny of the symbiotic genes nodA and nifH, and by performing nodulation assays. The isolates had highly conserved symbiotic genes and were classified into nine genospecies belonging to the genera Ensifer, Agrobacterium, Neorhizobium and Rhizobium. A unique community structure was detected in the rhizobia associated with S. cannabina in the saline-alkaline soils that was characterized by five novel genospecies and four defined species. In addition, Ensifer sp. I was the predominant rhizobia in YRD, whereas Ensifer meliloti and Neorhizobium huautlense were the dominant species in RDC. Therefore, the study demonstrated for the first time that this plant strongly selected the symbiotic gene background but not the genomic background of its microsymbionts. In addition, biogeographic patterns existed in the rhizobial populations associated with S. cannabina, which were mainly correlated with pH and salinity, as well as the mineral nutrient contents. This study provided novel information concerning the interaction between soil conditions, host plant and rhizobia, in addition to revealing the diversity of S. cannabina rhizobia in saline-alkaline soils. PMID:27061259

  12. Prognosis of Thyroid Nodules in Individuals Living in the Zhitomir Region of Ukraine

    PubMed Central

    Hayashida, Naomi; Sekitani, Yui; Takahashi, Jumpei; Kozlovsky, Alexander A.; Gutevych, Oleksandr K.; Saiko, Aleksey S.; Nirova, Nina V.; Petrova, Anjela A.; Rafalskiy, Ruslan M.; Chorny, Sergey A.; Daniliuk, Valery V.; Anami, Masanobu; Yamashita, Shunichi; Takamura, Noboru

    2012-01-01

    Objective After the accident at the Chernobyl Nuclear Power Plant (CNPP), the incidence of thyroid cancer increased among children. Recently, a strong relationship between solid thyroid nodules and the incidence of thyroid cancer was shown in atomic bomb survivors. To assess the prognosis of benign thyroid nodules in individuals living in the Zhitomir region of Ukraine, around the CNPP, we conducted a follow-up investigation of screening data from 1991 to 2000 in the Ukraine. Patients and Methods Participants of this study were 160 inhabitants with thyroid nodules (nodule group) and 160 inhabitants without thyroid nodules (normal control group) intially identified by ultrasonography from 1991 to 2000. All participants were aged 0 to 10 years old and lived in the same area at the time of the accident. We performed follow-up screening of participants and assessed thyroid nodules by fine needle aspiration biopsy. Results Among the nodule group participants, the number and size of nodules were significantly increased at the follow-up screening compared with the initial screening. No thyroid nodules were observed among the normal control group participants. The prevalence of thyroid abnormality, especially nodules that could be cancerous (malignant or suspicious by fine needle aspiration biopsy), was 7.5% in the nodule group and 0% in the normal control group (P<0.001). Conclusions Our study indicated that a thyroid nodule in childhood is a prognostic factor associated with an increase in the number and size of nodules in individuals living in the Zhitomir region of Ukraine. PMID:23209797

  13. microRNA160 dictates stage-specific auxin and cytokinin sensitivities and directs soybean nodule development.

    PubMed

    Nizampatnam, Narasimha Rao; Schreier, Spencer John; Damodaran, Suresh; Adhikari, Sajag; Subramanian, Senthil

    2015-10-01

    Legume nodules result from coordinated interactions between the plant and nitrogen-fixing rhizobia. The phytohormone cytokinin promotes nodule formation, and recent findings suggest that the phytohormone auxin inhibits nodule formation. Here we show that microRNA160 (miR160) is a key signaling element that determines the auxin/cytokinin balance during nodule development in soybean (Glycine max). miR160 appears to promote auxin activity by suppressing the levels of the ARF10/16/17 family of repressor ARF transcription factors. Using quantitative PCR assays and a fluorescence miRNA sensor, we show that miR160 levels are relatively low early during nodule formation and high in mature nodules. We had previously shown that ectopic expression of miR160 in soybean roots led to a severe reduction in nodule formation, coupled with enhanced sensitivity to auxin and reduced sensitivity to cytokinin. Here we show that exogenous cytokinin restores nodule formation in miR160 over-expressing roots. Therefore, low miR160 levels early during nodule development favor cytokinin activity required for nodule formation. Suppression of miR160 levels using a short tandem target mimic (STTM160) resulted in reduced sensitivity to auxin and enhanced sensitivity to cytokinin. In contrast to miR160 over-expressing roots, STTM160 roots had increased nodule formation, but nodule maturation was significantly delayed. Exogenous auxin partially restored proper nodule formation and maturation in STTM160 roots, suggesting that high miR160 activity later during nodule development favors auxin activity and promotes nodule maturation. Therefore, miR160 dictates developmental stage-specific sensitivities to auxin and cytokinin to direct proper nodule formation and maturation in soybean. PMID:26287653

  14. Rhizobial Ecology of the Woody Legume Mesquite (Prosopis glandulosa) in the Sonoran Desert

    PubMed Central

    Jenkins, Michael B.; Virginia, Ross A.; Jarrell, Wesley M.

    1987-01-01

    Soil samples were collected from the surface (0 to 0.6 m) and phreatic (3.9 to 4.5 m) root systems of a Prosopis glandulosa woodland in the Sonoran Desert of southern California. P. glandulosa seedlings were inoculated with these soils, and rhizobia were isolated from nodules. The phreatic soil, characterized by constant moisture and temperature but low nutrient availability, favored slow-growing (SG) isolates as nodule occupants (85%). SG isolates from the surface and phreatic soil were distinct based on differences in colony morphology. Isolates from the surface soil, characterized by high nutrient availability and widely fluctuating water content and temperature, were equally represented by fast-growing and SG rhizobia. Most SG isolates (83%) had nodule relative efficiencies of <0.80, whereas 54% of the fast-growing isolates had relative efficiency values of >0.80. PMID:16347264

  15. Contribution of NFP LysM Domains to the Recognition of Nod Factors during the Medicago truncatula/Sinorhizobium meliloti Symbiosis

    PubMed Central

    Bensmihen, Sandra; de Billy, Françoise; Gough, Clare

    2011-01-01

    The root nodule nitrogen fixing symbiosis between legume plants and soil bacteria called rhizobia is of great agronomical and ecological interest since it provides the plant with fixed atmospheric nitrogen. The establishment of this symbiosis is mediated by the recognition by the host plant of lipo-chitooligosaccharides called Nod Factors (NFs), produced by the rhizobia. This recognition is highly specific, as precise NF structures are required depending on the host plant. Here, we study the importance of different LysM domains of a LysM-Receptor Like Kinase (LysM-RLK) from Medicago truncatula called Nod factor perception (NFP) in the recognition of different substitutions of NFs produced by its symbiont Sinorhizobium meliloti. These substitutions are a sulphate group at the reducing end, which is essential for host specificity, and a specific acyl chain at the non-reducing end, that is critical for the infection process. The NFP extracellular domain (ECD) contains 3 LysM domains that are predicted to bind NFs. By swapping the whole ECD or individual LysM domains of NFP for those of its orthologous gene from pea, SYM10 (a legume plant that interacts with another strain of rhizobium producing NFs with different substitutions), we showed that NFP is not directly responsible for specific recognition of the sulphate substitution of S. meliloti NFs, but probably interacts with the acyl substitution. Moreover, we have demonstrated the importance of the NFP LysM2 domain for rhizobial infection and we have pinpointed the importance of a single leucine residue of LysM2 in that step of the symbiosis. Together, our data put into new perspective the recognition of NFs in the different steps of symbiosis in M. truncatula, emphasising the probable existence of a missing component for early NF recognition and reinforcing the important role of NFP for NF recognition during rhizobial infection. PMID:22087221

  16. Cicer canariense, an endemic legume to the Canary Islands, is nodulated in mainland Spain by fast-growing strains from symbiovar trifolii phylogenetically related to Rhizobium leguminosarum.

    PubMed

    Martínez-Hidalgo, Pilar; Flores-Félix, José-David; Menéndez, Esther; Rivas, Raúl; Carro, Lorena; Mateos, Pedro F; Martínez-Molina, Eustoquio; León-Barrios, Milagros; Velázquez, Encarna

    2015-07-01

    Cicer canariense is a threatened endemic legume from the Canary Islands where it can be nodulated by mesorhizobial strains from the symbiovar ciceri, which is the common worldwide endosymbiont of Cicer arietinum linked to the genus Mesorhizobium. However, when C. canariense was cultivated in a soil from mainland Spain, where the symbiovar ciceri is present, only fast-growing rhizobial strains were unexpectedly isolated from its nodules. These strains were classified into the genus Rhizobium by analysis of the recA and atpD genes, and they were phylogenetically related to Rhizobium leguminosarum. The analysis of the nodC gene showed that the isolated strains belonged to the symbiovar trifolii that harbored a nodC allele (β allele) different to that harbored by other strains from this symbiovar. Nodulation experiments carried out with the lacZ-labeled strain RCCHU01, representative of the β nodC allele, showed that it induced curling of root hairs, infected them through infection threads, and formed typical indeterminate nodules where nitrogen fixation took place. This represents a case of exceptional performance between the symbiovar trifolii and a legume from the tribe Cicereae that opens up new possibilities and provides new insights into the study of rhizobia-legume symbiosis. PMID:26032249

  17. Rhizobia from Lanzarote, the Canary Islands, That Nodulate Phaseolus vulgaris Have Characteristics in Common with Sinorhizobium meliloti Isolates from Mainland Spain▿

    PubMed Central

    Zurdo-Piñeiro, José Luis; García-Fraile, Paula; Rivas, Raúl; Peix, Alvaro; León-Barrios, Milagros; Willems, Anne; Mateos, Pedro Francisco; Martínez-Molina, Eustoquio; Velázquez, Encarna; van Berkum, Peter

    2009-01-01

    The stable, low-molecular-weight (LMW) RNA fractions of several rhizobial isolates of Phaseolus vulgaris grown in the soil of Lanzarote, an island of the Canary Islands, were identical to a less-common pattern found within Sinorhizobium meliloti (assigned to group II) obtained from nodules of alfalfa and alfalfa-related legumes grown in northern Spain. The P. vulgaris isolates and the group II LMW RNA S. meliloti isolates also were distinguishable in that both had two conserved inserts of 20 and 46 bp in the 16S-23S internal transcribed spacer region that were not present in other strains of S. meliloti. The isolates from P. vulgaris nodulated bean but not Medicago sativa, while those recovered from Medicago, Melilotus, and Trigonella spp. nodulated both host legumes. The bean isolates also were distinguished from those of Medicago, Melilotus, and Trigonella spp. by nodC sequence analysis. The nodC sequences of the bean isolates were most similar to those reported for S. meliloti bv. mediterranense and Sinorhizobium fredii bv. mediterranense (GenBank accession numbers DQ333891 and AF217267, respectively). None of the evidence placed the bean isolates from Lanzarote in the genus Rhizobium, which perhaps is inconsistent with seed-borne transmission of Rhizobium etli from the Americas to the Canaries as an explanation for the presence of bean-nodulating rhizobia in soils of Lanzarote. PMID:19218416

  18. Positioning the nodule, the hormone dictum

    PubMed Central

    Ding, Yiliang

    2009-01-01

    The formation of a nitrogen-fixing nodule involves two diverse developmental processes in the legume root: infection thread initiation in epidermal cells and nodule primordia formation in the cortex. Several plant hormones have been reported to positively or negatively regulate nodulation. These hormones function at different stages in the nodulation process and may facilitate the coordinated development of the epidermal and cortical developmental programs that are necessary to allow bacterial infection into the developing nodule. In this paper, we review and discuss how the tissue specific nature of hormonal action dictates where, when and how a nodule is formed. PMID:19649179

  19. Positioning the nodule, the hormone dictum.

    PubMed

    Ding, Yiliang; Oldroyd, Giles E D

    2009-02-01

    The formation of a nitrogen-fixing nodule involves two diverse developmental processes in the legume root: infection thread initiation in epidermal cells and nodule primordia formation in the cortex. Several plant hormones have been reported to positively or negatively regulate nodulation. These hormones function at different stages in the nodulation process and may facilitate the coordinated development of the epidermal and cortical developmental programs that are necessary to allow bacterial infection into the developing nodule. In this paper, we review and discuss how the tissue specific nature of hormonal action dictates where, when and how a nodule is formed. PMID:19649179

  20. New Nodule-Newer Etiology

    PubMed Central

    Mehta, Atul C; Wang, Juan; Abuqayyas, Sami; Garcha, Puneet; Lane, Charles Randy; Tsuang, Wayne; Budev, Marie; Akindipe, Olufemi

    2016-01-01

    AIM: To evaluate frequency and temporal relationship between pulmonary nodules (PNs) and transbronchial biopsy (TBBx) among lung transplant recipients (LTR). METHODS: We retrospectively reviewed 100 records of LTR who underwent flexible bronchoscopy (FB) with TBBx, looking for the appearance of peripheral pulmonary nodule (PPN). If these patients had chest radiographs within 50 d of FB, they were included in the study. Data was compared with 30 procedures performed among non-transplant patients. Information on patient’s demographics, antirejection medications, anticoagulation, indication and type of lung transplantation, timing of the FB and the appearance and disappearance of the nodules and its characteristics were gathered. RESULTS: Nineteen new PN were found in 13 procedures performed on LTR and none among non-transplant patients. Nodules were detected between 4-47 d from the procedure and disappeared within 84 d after appearance without intervention. CONCLUSION: FB in LTR is associated with development of new, transient PPN at the site of TBBx in 13% of procedures. We hypothesize that these nodules are related to local hematoma and impaired lymphatic drainage. Close observation is a reasonable management approach. PMID:27011920

  1. Interaction of a rhizobial DNA-binding protein with the promoter region of a plant leghemoglobin gene

    SciTech Connect

    Welters, P.; Metz, B.; Felix, G.; Palme, K. ); Szczyglowski, K. ); Bruijn, F.J. de Michigan State Univ., East Lansing, MI )

    1993-08-01

    A nucleotide sequence was identified approximately 650 bp upstream of the Sesbania rostrata leghemoglobin gene Srglb3 start codon, which interacts specifically with a proteinaceous DNA-binding factor found in nodule extracts but not in extracts from leaves or root. The binding site for this factor was delimited using footprinting techniques. The DNA-binding activity of this factor was found to be heat stable, dependent on divalent cations, and derived from the (infecting) Azorhizobium caulinodans bacteria or bacteroids (A. caulinodans bacterial binding factor 1, AcBBF1). A 9- to 10-kD protein was isolated from a free-living culture of A. caulinodans that co-purifies with the DNA-binding activity (A. caulinodans bacterial binding protein 1, AcBBP1) and interacts specifically with its target (S. rostrata bacterial binding site 1, SrBBS1). The amino acid sequence of the N-terminal 27 residues of AcBBP1 was determined and was found to share significant similarity (46% identity; 68% similarity) with a domain of the herpes simplex virus major DNA-binding protein infected cell protein 8(ICP8). An insertion mutation in the SrBBS1 was found to result in a substantial reduction of the expression of a Srglb3-gus reporter gene fusion in nodules of transgenic Lotus corniculatus plants, suggesting a role for this element in Srglb3 promoter activity. Based on these results, the authors propose that (a) bacterial transacting factor(s) may play a role in infected cell-specific expression of the symbiotically induced plant lb genes. 70 refs., 11 figs.

  2. Genetic diversity and symbiotic compatibility among rhizobial strains and Desmodium incanum and Lotus spp. plants.

    PubMed

    Granada, Camille E; Strochein, Marcos; Vargas, Luciano K; Bruxel, Manuela; de Sá, Enilson Luiz Saccol; Passaglia, Luciane M P

    2014-06-01

    This work aimed to evaluate the symbiotic compatibility and nodulation efficiency of rhizobia isolated from Desmodium incanum, Lotus corniculatus, L. subbiflorus, L. uliginosus and L. glaber plants by cross-inoculation. Twelve reference strains and 21 native isolates of rhizobia were genetically analyzed by the BOX-PCR technique, which showed a high genetic diversity among the rhizobia studied. The isolates were also characterized based on their production of indolic compounds and siderophores, as well as on their tolerance to salinity. Fifteen of the 33 rhizobia analyzed were able to produce indolic compounds, whereas 13 produced siderophores. All the tested rhizobia were sensitive to high salinity, although some were able to grow in solutions of up to 2% NaCl. Most of the native rhizobia isolated from L. uliginosus were able to induce nodulation in all plant species studied. In a greenhouse experiment using both D. incanum and L. corniculatus plants, the rhizobia isolate UFRGS Lu2 promoted the greatest plant growth. The results demonstrate that there are native rhizobia in the soils of southern Brazil that have low host specificity and are able to induce nodulation and form active nodules in several plant species. PMID:25071405

  3. Genetic diversity and symbiotic compatibility among rhizobial strains and Desmodium incanum and Lotus spp. plants

    PubMed Central

    Granada, Camille E.; Strochein, Marcos; Vargas, Luciano K.; Bruxel, Manuela; de Sá, Enilson Luiz Saccol; Passaglia, Luciane M.P.

    2014-01-01

    This work aimed to evaluate the symbiotic compatibility and nodulation efficiency of rhizobia isolated from Desmodium incanum, Lotus corniculatus, L. subbiflorus, L. uliginosus and L. glaber plants by cross-inoculation. Twelve reference strains and 21 native isolates of rhizobia were genetically analyzed by the BOX-PCR technique, which showed a high genetic diversity among the rhizobia studied. The isolates were also characterized based on their production of indolic compounds and siderophores, as well as on their tolerance to salinity. Fifteen of the 33 rhizobia analyzed were able to produce indolic compounds, whereas 13 produced siderophores. All the tested rhizobia were sensitive to high salinity, although some were able to grow in solutions of up to 2% NaCl. Most of the native rhizobia isolated from L. uliginosus were able to induce nodulation in all plant species studied. In a greenhouse experiment using both D. incanum and L. corniculatus plants, the rhizobia isolate UFRGS Lu2 promoted the greatest plant growth. The results demonstrate that there are native rhizobia in the soils of southern Brazil that have low host specificity and are able to induce nodulation and form active nodules in several plant species. PMID:25071405

  4. Influence of atmospheric [CO2] on growth, carbon allocation and cost of plant tissues on leaf nitrogen concentration maintenance in nodulated Medicago sativa

    NASA Astrophysics Data System (ADS)

    Pereyra, Gabriela; Hartmann, Henrik; Ziegler, Waldemar; Michalzik, Beate; Gonzalez-Meler, Miquel; Trumbore, Susan

    2015-04-01

    Plant carbon (C) allocation and plant metabolic processes (i.e. photosynthesis and respiration) can be affected by changes in C availability, for example from changing atmospheric [CO2]. In nodulated plants, C availability may also influence nitrogen (N) fixation by bacteriods. But C allocation and N fixation are often studied independently and hence do not allow elucidating interactive effects. We investigated how different atmospheric [CO2] (Pleistocene: 170 ppm, ambient: 400 ppm and projected future: 700 ppm) influence plant growth, allocation to nodules, and the ratio of photosynthesis-to-respiration (R:A) as an indicator of C cost in Medicago sativa inoculated with Ensifer meliloti. M. sativa grew c. 38% more nodules at 400 ppm and 700 ppm than at 170 ppm. However, ratios of above- and belowground plant biomass to nodule biomass were constant over time and independent of atmospheric [CO2]. Total non-structural carbohydrate concentrations were not significantly different between plants grown at 400 and 700 ppm, but were four to five-fold higher than in 170 ppm plants. Leaf level N concentration was similar across treatments, but N-based photosynthetic rates were 82% and 93% higher in leaves of plants grown at 400 and 700 ppm, respectively, than plants grown at 170 ppm. In addition, leaf R:A was greater (48% or 55%) in plants grown at 170 ppm than plants grown at 400 and 700 ppm. Similarly, the greatest proportion of assimilated CO2 released by root respiration occurred in rhizobial plants growing at 170 ppm. Our results suggest that C limitation in nodulated Medicago sativa plants did not influence C allocation to nodule biomass but caused a proportionally greater allocation of C to belowground respiration, most likely to bacteriods. This suggests that N tissue concentration was maintained at low [CO2] by revving up bacteriod metabolism and at the expense of non-structural carbohydrate reserves.

  5. Interaction of root nodule size and oxygen pressure on the rate of nitrogen fixation by cowpea and peanut

    SciTech Connect

    Sen, D.; Weaver, R.W.

    1987-04-01

    Size and anatomical features of nodules influence the rate of O/sub 2/ diffusion into nodules. Availability of oxygen can be a limiting factor in nitrogen fixation. Larger nodules have thicker cortices and low surface to volume ratio leading to lower rates of gaseous diffusion. Increased oxygen pressure in the environment alters the rate of nitrogen fixation but the rate of change may depend on the nodule size. This was investigated by measuring /sup 15/N/sub 2/ incorporation into nodules. Root nodules from 38 day old cowpea and peanut plants were collected and sorted into size groups having diameters of >3 mm, 2-3 mm, and just below 2 mm. Samples of each size group were enclosed in tubes and exposed to various combination of oxygen (8-28%) and /sup 15/N/sub 2/. With higher O/sub 2/ pressure all nodules showed increased N/sub 2/ fixation but the largest nodules showed the maximum increase. Specific activity of larger nodules was higher for N/sub 2/ fixation. For the sizes of nodules examined the largest nodules did not reflect any of the disadvantages of the large size but the benefits of higher rates of O/sub 2/ entry was evident.

  6. Isolated Rheumatoid Nodule of the Achilles.

    PubMed

    Spicer, Paul J; Broussard, Gerald; Beaman, Francesca

    2016-06-01

    Approximately 20% to 25% of patients with rheumatoid arthritis have rheumatoid nodules. These nodules most commonly involve the soft tissues of the upper extremity, particularly adjacent to the olecranon. We present an uncommon case of a solitary rheumatoid nodule arising from the paratenon of the Achilles tendon with ultrasound and magnetic resonance images. PMID:26086458

  7. Basis for the competitiveness of Rhizobium japonicum in nodulation of soybean. Final progress report

    SciTech Connect

    Evans, W.R.; Bauer, W.D.

    1986-07-30

    This study sought to identify molecular, genetic and environmental factors most crucial to the ability of an inoculated strain of rhizobia to nodulate soybean roots in the face of competition from indigenous microorganisms. Co-inoculation of a more efficient strain with a less-efficient strain resulted in the more efficient strain occupying a higher percentage of nodules. When culture conditions became less stringent the less efficient strain became more competitive. The number of infections formed was related in a direct manner to nodulation efficiency. The strain which was more nodulation efficient also was more infection efficient. That the number of infections per se, as determined in a single inoculum, can not be the only factor in determining the competency was indicated by experiments in which one strain formed more total infection yet nodule occupancy was equally distributed. 5 figs., 9 tabs.

  8. Evaluation of the thyroid nodule

    SciTech Connect

    Cannon, C.R.

    1986-05-01

    Evaluation of thyroid nodules challenges the most astute clinician. The history and the physical examination often identify those patients who require immediate surgical management. In other patients, time-honored thyroid function studies and thyroid scanning are helpful. Fine needle aspiration and computed tomography are also valuable in the diagnostic work-up.

  9. Incidental nodule management-should there be a formal process?

    PubMed

    Sethi, Sonali; Parrish, Scott

    2016-07-01

    Indeterminate pulmonary nodules are commonly encountered and often result in costly and invasive procedures that eventually turn out to be unnecessary. Current prediction models can help to estimate the pretest probability of cancer and assist in determining a strategy of observation with serial imaging for a low pretest probability of cancer, and a more aggressive approach for those patients with a high pretest probability. However, the majority of patients will have an intermediate pretest probability which becomes complex. Decisions for further management are often based on preference by the clinician with the majority of physicians not following current guidelines in the management of pulmonary nodules. Poor adherence to pulmonary nodule guidelines is multifactorial with a variety of factors coming into play. These include inappropriate advice given by the radiologist, patient age, comorbidities, patient preference, and physician's technical skill all influencing the decision making. PMID:27606078

  10. Incidental nodule management—should there be a formal process?

    PubMed Central

    2016-01-01

    Indeterminate pulmonary nodules are commonly encountered and often result in costly and invasive procedures that eventually turn out to be unnecessary. Current prediction models can help to estimate the pretest probability of cancer and assist in determining a strategy of observation with serial imaging for a low pretest probability of cancer, and a more aggressive approach for those patients with a high pretest probability. However, the majority of patients will have an intermediate pretest probability which becomes complex. Decisions for further management are often based on preference by the clinician with the majority of physicians not following current guidelines in the management of pulmonary nodules. Poor adherence to pulmonary nodule guidelines is multifactorial with a variety of factors coming into play. These include inappropriate advice given by the radiologist, patient age, comorbidities, patient preference, and physician’s technical skill all influencing the decision making. PMID:27606078

  11. Lung nodules detection in chest radiography: image components analysis

    NASA Astrophysics Data System (ADS)

    Luo, Tao; Mou, Xuanqin; Yang, Ying; Yan, Hao

    2009-02-01

    We aimed to evaluate the effect of different components of chest image on performances of both human observer and channelized Fisher-Hotelling model (CFH) in nodule detection task. Irrelevant and relevant components were separated from clinical chest radiography by employing Principal Component Analysis (PCA) methods. Human observer performance was evaluated in two-alternative forced-choice (2AFC) on original clinical images and anatomical structure only images obtained by PCA methods. Channelized Fisher-Hotelling model with Laguerre-Gauss basis function was evaluated to predict human performance. We show that relevant component is the primary factor influencing on nodule detection in chest radiography. There is obvious difference of detectability between human observer and CFH model for nodule detection in images only containing anatomical structure. CFH model should be used more carefully.

  12. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes.

    PubMed

    Chaintreuil, Clémence; Rivallan, Ronan; Bertioli, David J; Klopp, Christophe; Gouzy, Jérôme; Courtois, Brigitte; Leleux, Philippe; Martin, Guillaume; Rami, Jean-François; Gully, Djamel; Parrinello, Hugues; Séverac, Dany; Patrel, Delphine; Fardoux, Joël; Ribière, William; Boursot, Marc; Cartieaux, Fabienne; Czernic, Pierre; Ratet, Pascal; Mournet, Pierre; Giraud, Eric; Arrighi, Jean-François

    2016-08-01

    Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far focused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n = 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a basis for a genome sequencing project and pave the way for forward genetic analysis of symbiosis in A. evenia. PMID:27298380

  13. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes

    PubMed Central

    Chaintreuil, Clémence; Rivallan, Ronan; Bertioli, David J.; Klopp, Christophe; Gouzy, Jérôme; Courtois, Brigitte; Leleux, Philippe; Martin, Guillaume; Rami, Jean-François; Gully, Djamel; Parrinello, Hugues; Séverac, Dany; Patrel, Delphine; Fardoux, Joël; Ribière, William; Boursot, Marc; Cartieaux, Fabienne; Czernic, Pierre; Ratet, Pascal; Mournet, Pierre; Giraud, Eric; Arrighi, Jean-François

    2016-01-01

    Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far focused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n = 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a basis for a genome sequencing project and pave the way for forward genetic analysis of symbiosis in A. evenia. PMID:27298380

  14. “The thing is not knowing”: Patients' perspectives on surveillance of an indeterminate pulmonary nodule

    PubMed Central

    Wiener, Renda Soylemez; Gould, Michael K.; Woloshin, Steven; Schwartz, Lisa M.; Clark, Jack A.

    2013-01-01

    Background The hundreds of thousands of patients found to have a potentially malignant pulmonary nodule each year are faced with tremendous uncertainty regarding what the nodule is and how it should be evaluated. Objective To explore Patients' responses to the detection and evaluation of a pulmonary nodule Design Qualitative study based on 4 focus group discussions. We performed inductive analysis using principles of grounded theory to identify themes relating to responses to the nodule and strategies to manage uncertainty. Setting and Participants 22 patients from 2 medical centers who were undergoing surveillance for an indeterminate pulmonary nodule Results Patient responses to an indeterminate pulmonary nodule were varied and evolved over time. Although almost all patients reported an initial fear about cancer, subsequent depictions of the nodule diverged into 4 types defined on two dimensions: cognitive (“it's cancer” vs. “I don't know what it is” vs. “it's nothing serious”) and emotional (anxiety vs. equanimity). Most eventually accepted that the nodule was unlikely to be malignant; however, some remained anxious, convinced the nodule could turn into cancer at any time and should be aggressively monitored for life. Patients used results of surveillance tests as well as their own strategies (e.g., vigilance for symptoms, information-seeking, contemplating and controlling modifiable risk factors, avoidance, faith) to manage uncertainty. Conclusions Surveillance for a pulmonary nodule can weigh heavily on some patients for months or years. Our findings may help clinicians prepare patients with a newly detected pulmonary nodule for the burden of the prolonged uncertainty of surveillance. PMID:23252477

  15. Increase of Natural 15N Enrichment of Soybean Nodules with Mean Nodule Mass 1

    PubMed Central

    Shearer, Georgia; Bryan, Barbara A.; Kohl, Daniel H.

    1984-01-01

    The 15N abundance of soybean (Glycine max L. Merrill var Harosoy) nodules is usually greater than it is for other tissues or for atmospheric N2. Results of experiments in which nodules were separated by size show that the magnitude of the 15N enrichment is correlated with nodule mass. The results support the hypothesis that 15N enrichment of nodules results from differential N isotopic fractionation for synthesis of nodule tissue versus synthesis of compounds for export from the nodule. The physiological significance of this hypothesis is that it requires that a substantial fraction of the N for nodule tissue synthesis in 15N-enriched nodules be N recently fixed within the same nodule. PMID:16663917

  16. Decision making in patients with pulmonary nodules.

    PubMed

    Ost, David E; Gould, Michael K

    2012-02-15

    Integrating current evidence with fundamental concepts from decision analysis suggests that management of patients with pulmonary nodules should begin with estimating the pretest probability of cancer from the patient's clinical risk factors and computed tomography characteristics. Then, the consequences of treatment should be considered, by comparing the benefits of surgery if the patient has lung cancer with the potential harm if the patient does not have cancer. This analysis determines the "treatment threshold," which is the point around which the decision centers. This varies widely among patients depending on their cardiopulmonary reserve, comorbidities, and individual preferences. For patients with a very low probability of cancer, careful observation with serial computed tomography is warranted. For those with a high probability of cancer, surgical diagnosis is warranted. For patients in the intermediate range of probabilities, either computed tomography-guided fine-needle aspiration biopsy or positron emission tomography, possibly followed by computed tomography-guided fine-needle aspiration biopsy, is best. Patient preferences should be considered because the absolute difference in outcome between strategies may be small. The optimal approach to the management of patients with pulmonary nodules is evolving as technologies develop. Areas of uncertainty include quantifying the hazard of delayed diagnosis; determining the optimal duration of follow-up for ground-glass and semisolid opacities; establishing the roles of volumetric imaging, advanced bronchoscopic technologies, and limited surgical resections; and calculating the cost-effectiveness of different strategies. PMID:21980032

  17. A Report of 10 Individuals with Weathering Nodules and Review of the Literature

    PubMed Central

    Udkoff, Jeremy; Cohen, Philip R

    2016-01-01

    Weathering nodules are a benign skin condition that usually present as papules on the helices of patients with significant prior sun exposure. They are easily recognized clinically and blanch upon application of pressure to the adjacent helical rim: a positive blanch sign. We describe the clinical presentation of weathering nodules in 10 patients, nine men and one woman, aging from 38 to 70 (median 59), and their associated risk factors. Eight patients had a history of actinic keratosis, three had a history of nonmelanoma skin cancer, and all patients had increased Sun exposure through outdoor activities. Weathering nodules are rarely mentioned in the literature and may be confused with other cutaneous disorders. Therefore, it is paramount for clinicians to become familiar with weathering nodules and include them in the differential diagnosis of ear nodules. Appropriate diagnosis will help avoid unnecessary biopsies while reassuring the patient that the lesions are benign. PMID:27512191

  18. A Report of 10 Individuals with Weathering Nodules and Review of the Literature.

    PubMed

    Udkoff, Jeremy; Cohen, Philip R

    2016-01-01

    Weathering nodules are a benign skin condition that usually present as papules on the helices of patients with significant prior sun exposure. They are easily recognized clinically and blanch upon application of pressure to the adjacent helical rim: a positive blanch sign. We describe the clinical presentation of weathering nodules in 10 patients, nine men and one woman, aging from 38 to 70 (median 59), and their associated risk factors. Eight patients had a history of actinic keratosis, three had a history of nonmelanoma skin cancer, and all patients had increased Sun exposure through outdoor activities. Weathering nodules are rarely mentioned in the literature and may be confused with other cutaneous disorders. Therefore, it is paramount for clinicians to become familiar with weathering nodules and include them in the differential diagnosis of ear nodules. Appropriate diagnosis will help avoid unnecessary biopsies while reassuring the patient that the lesions are benign. PMID:27512191

  19. Phosphorylation-Dependent Regulation of G-Protein Cycle during Nodule Formation in Soybean[OPEN

    PubMed Central

    2015-01-01

    Signaling pathways mediated by heterotrimeric G-protein complexes comprising Gα, Gβ, and Gγ subunits and their regulatory RGS (Regulator of G-protein Signaling) protein are conserved in all eukaryotes. We have shown that the specific Gβ and Gγ proteins of a soybean (Glycine max) heterotrimeric G-protein complex are involved in regulation of nodulation. We now demonstrate the role of Nod factor receptor 1 (NFR1)-mediated phosphorylation in regulation of the G-protein cycle during nodulation in soybean. We also show that during nodulation, the G-protein cycle is regulated by the activity of RGS proteins. Lower or higher expression of RGS proteins results in fewer or more nodules, respectively. NFR1 interacts with RGS proteins and phosphorylates them. Analysis of phosphorylated RGS protein identifies specific amino acids that, when phosphorylated, result in significantly higher GTPase accelerating activity. These data point to phosphorylation-based regulation of G-protein signaling during nodule development. We propose that active NFR1 receptors phosphorylate and activate RGS proteins, which help maintain the Gα proteins in their inactive, trimeric conformation, resulting in successful nodule development. Alternatively, RGS proteins might also have a direct role in regulating nodulation because overexpression of their phospho-mimic version leads to partial restoration of nodule formation in nod49 mutants. PMID:26498905

  20. A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria

    PubMed Central

    Zgadzaj, Rafal; James, Euan K.; Kelly, Simon; Kawaharada, Yasuyuki; de Jonge, Nadieh; Jensen, Dorthe B.; Madsen, Lene H.; Radutoiu, Simona

    2015-01-01

    Legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules. For the symbionts, a complex genetic mechanism that allows mutual recognition and plant infection has emerged from genetic studies under axenic conditions. In contrast, little is known about the mechanisms controlling the endophytic infection. Here we investigate the contribution of both the host and the symbiotic microbe to endophyte infection and development of mixed colonised nodules in Lotus japonicus. We found that infection threads initiated by Mesorhizobium loti, the natural symbiont of Lotus, can selectively guide endophytic bacteria towards nodule primordia, where competent strains multiply and colonise the nodule together with the nitrogen-fixing symbiotic partner. Further co-inoculation studies with the competent coloniser, Rhizobium mesosinicum strain KAW12, show that endophytic nodule infection depends on functional and efficient M. loti-driven Nod factor signalling. KAW12 exopolysaccharide (EPS) enabled endophyte nodule infection whilst compatible M. loti EPS restricted it. Analysis of plant mutants that control different stages of the symbiotic infection showed that both symbiont and endophyte accommodation within nodules is under host genetic control. This demonstrates that when legume plants are exposed to complex communities they selectively regulate access and accommodation of bacteria occupying this specialized environmental niche, the root nodule. PMID:26042417

  1. Automatic lung nodule classification with radiomics approach

    NASA Astrophysics Data System (ADS)

    Ma, Jingchen; Wang, Qian; Ren, Yacheng; Hu, Haibo; Zhao, Jun

    2016-03-01

    Lung cancer is the first killer among the cancer deaths. Malignant lung nodules have extremely high mortality while some of the benign nodules don't need any treatment .Thus, the accuracy of diagnosis between benign or malignant nodules diagnosis is necessary. Notably, although currently additional invasive biopsy or second CT scan in 3 months later may help radiologists to make judgments, easier diagnosis approaches are imminently needed. In this paper, we propose a novel CAD method to distinguish the benign and malignant lung cancer from CT images directly, which can not only improve the efficiency of rumor diagnosis but also greatly decrease the pain and risk of patients in biopsy collecting process. Briefly, according to the state-of-the-art radiomics approach, 583 features were used at the first step for measurement of nodules' intensity, shape, heterogeneity and information in multi-frequencies. Further, with Random Forest method, we distinguish the benign nodules from malignant nodules by analyzing all these features. Notably, our proposed scheme was tested on all 79 CT scans with diagnosis data available in The Cancer Imaging Archive (TCIA) which contain 127 nodules and each nodule is annotated by at least one of four radiologists participating in the project. Satisfactorily, this method achieved 82.7% accuracy in classification of malignant primary lung nodules and benign nodules. We believe it would bring much value for routine lung cancer diagnosis in CT imaging and provide improvement in decision-support with much lower cost.

  2. CYTOKININ OXIDASE/DEHYDROGENASE3 Maintains Cytokinin Homeostasis during Root and Nodule Development in Lotus japonicus1[OPEN

    PubMed Central

    Heckmann, Anne B.; Kelly, Simon

    2016-01-01

    Cytokinins are required for symbiotic nodule development in legumes, and cytokinin signaling responses occur locally in nodule primordia and in developing nodules. Here, we show that the Lotus japonicus Ckx3 cytokinin oxidase/dehydrogenase gene is induced by Nod factor during the early phase of nodule initiation. At the cellular level, pCkx3::YFP reporter-gene studies revealed that the Ckx3 promoter is active during the first cortical cell divisions of the nodule primordium and in growing nodules. Cytokinin measurements in ckx3 mutants confirmed that CKX3 activity negatively regulates root cytokinin levels. Particularly, tZ and DHZ type cytokinins in both inoculated and uninoculated roots were elevated in ckx3 mutants, suggesting that these are targets for degradation by the CKX3 cytokinin oxidase/dehydrogenase. The effect of CKX3 on the positive and negative roles of cytokinin in nodule development, infection and regulation was further clarified using ckx3 insertion mutants. Phenotypic analysis indicated that ckx3 mutants have reduced nodulation, infection thread formation and root growth. We also identify a role for cytokinin in regulating nodulation and nitrogen fixation in response to nitrate as ckx3 phenotypes are exaggerated at increased nitrate levels. Together, these findings show that cytokinin accumulation is tightly regulated during nodulation in order to balance the requirement for cell divisions with negative regulatory effects of cytokinin on infection events and root development. PMID:26644503

  3. Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China

    PubMed Central

    Yao, Yao; Wang, Rui; Lu, Jun Kun; Wang, En Tao; Chen, Wen Xin

    2014-01-01

    The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia. PMID:25085491

  4. Genetic diversity and evolution of Bradyrhizobium populations nodulating Erythrophleum fordii, an evergreen tree indigenous to the southern subtropical region of China.

    PubMed

    Yao, Yao; Wang, Rui; Lu, Jun Kun; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2014-10-01

    The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia. PMID:25085491

  5. Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus–Mesorhizobium loti symbiosis

    PubMed Central

    Fukudome, Mitsutaka; Calvo-Begueria, Laura; Kado, Tomohiro; Osuki, Ken-ichi; Rubio, Maria Carmen; Murakami, Ei-ichi; Nagata, Maki; Kucho, Ken-ichi; Sandal, Niels; Stougaard, Jens; Becana, Manuel; Uchiumi, Toshiki

    2016-01-01

    Leghemoglobins transport and deliver O2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. However, the roles of other hemoglobins (Hbs) in the rhizobia–legume symbiosis are unclear. Several Lotus japonicus mutants affecting LjGlb1-1, a non-symbiotic class 1 Hb, have been used to study the function of this protein in symbiosis. Two TILLING alleles with single amino acid substitutions (A102V and E127K) and a LORE1 null allele with a retrotransposon insertion in the 5′-untranslated region (96642) were selected for phenotyping nodulation. Plants of all three mutant lines showed a decrease in long infection threads and nodules, and an increase in incipient infection threads. About 4h after inoculation, the roots of mutant plants exhibited a greater transient accumulation of nitric oxide (NO) than did the wild-type roots; nevertheless, in vitro NO dioxygenase activities of the wild-type, A102V, and E127K proteins were similar, suggesting that the mutated proteins are not fully functional in vivo. The expression of LjGlb1-1, but not of the other class 1 Hb of L. japonicus (LjGlb1-2), was affected during infection of wild-type roots, further supporting a specific role for LjGlb1-1. In conclusion, the LjGlb1-1 mutants reveal that this protein is required during rhizobial infection and regulates NO levels. PMID:27443280

  6. Medicago truncatula Natural Resistance-Associated Macrophage Protein1 Is Required for Iron Uptake by Rhizobia-Infected Nodule Cells1[OPEN

    PubMed Central

    Tejada-Jiménez, Manuel; Castro-Rodríguez, Rosario; Kryvoruchko, Igor; Lucas, M. Mercedes; Udvardi, Michael; Imperial, Juan; González-Guerrero, Manuel

    2015-01-01

    Iron is critical for symbiotic nitrogen fixation (SNF) as a key component of multiple ferroproteins involved in this biological process. In the model legume Medicago truncatula, iron is delivered by the vasculature to the infection/maturation zone (zone II) of the nodule, where it is released to the apoplast. From there, plasma membrane iron transporters move it into rhizobia-containing cells, where iron is used as the cofactor of multiple plant and rhizobial proteins (e.g. plant leghemoglobin and bacterial nitrogenase). MtNramp1 (Medtr3g088460) is the M. truncatula Natural Resistance-Associated Macrophage Protein family member, with the highest expression levels in roots and nodules. Immunolocalization studies indicate that MtNramp1 is mainly targeted to the plasma membrane. A loss-of-function nramp1 mutant exhibited reduced growth compared with the wild type under symbiotic conditions, but not when fertilized with mineral nitrogen. Nitrogenase activity was low in the mutant, whereas exogenous iron and expression of wild-type MtNramp1 in mutant nodules increased nitrogen fixation to normal levels. These data are consistent with a model in which MtNramp1 is the main transporter responsible for apoplastic iron uptake by rhizobia-infected cells in zone II. PMID:25818701

  7. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis.

    PubMed

    Crespo-Rivas, Juan C; Guefrachi, Ibtissem; Mok, Kenny C; Villaécija-Aguilar, José A; Acosta-Jurado, Sebastián; Pierre, Olivier; Ruiz-Sainz, José E; Taga, Michiko E; Mergaert, Peter; Vinardell, José M

    2016-09-01

    In rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation. PMID:26521863

  8. Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules

    PubMed Central

    Lu, Jun Kun; Dou, Ya Jing; Zhu, Ya Jie; Wang, Sheng Kun; Sui, Xin Hua

    2014-01-01

    Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium, which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium, indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium. Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (Tm). PMID:24585376

  9. [Root Nodule Bacteria Sinorhizobium meliloti: Tolerance to Salinity and Bacterial Genetic Determinants].

    PubMed

    Roumiantseva, M L; Muntyan, V S

    2015-01-01

    The theoretical and experimental data on salt tolerance of root nodule bacteria Sinorhizobium meliloti (Ensifer meliloti), an alfalfa symbiont, and on genetic determination of this feature are reviewed. Extensive data on the genes affecting adaptation of proteobacteria are provided, as well as on the groups of genes with activity depending on the osmolarity of the medium. Structural and functional polymorphism of the bet genes involved in betaine synthesis and transport in S. meliloti is discussed. The phenotypic and. genotypic polymorphism in 282 environmental rhizobial strains isolated from the centers of alfalfa diversity affected by aridity and salinity is discussed. The isolates from the Aral Sea area and northern Caucasus were shown to possess the betC gene represented by two types of alleles: the dominant A-type allele found in Rm 1021 and the less common divergent E-type allele, which was revealed in regions at the frequencies at the frequencies of 0.35 and 0.48, respectively. In the isolates with the salt-tolerant phenotype, which were isolated from root nodules and subsequently formed less effective symbioses with alfalfa, the frequency of E-type alleles was 2.5 times higher. Analysis of the nucleotide and amino acid sequences of the E-type allele of the betC gene revealed that establishment of this allele in the population was a result of positive selection. It is concluded that diversification of the functionally diverse bet genes occurring in S. meliloti affects the salt tolerance and symbiotic effectivity of rhizobia. PMID:26263687

  10. Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa.

    PubMed

    Steenkamp, Emma T; van Zyl, Elritha; Beukes, Chrizelle W; Avontuur, Juanita R; Chan, Wai Yin; Palmer, Marike; Mthombeni, Lunghile S; Phalane, Francina L; Sereme, T Karabo; Venter, Stephanus N

    2015-12-01

    Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native regions, relatively few taxa have been formally described. For example, the Cape Floristic Region of South Africa is thought to represent one of the major centres of diversity for the rhizobial members of Burkholderia, yet only five species have been described from legumes occurring in this region and numerous are still awaiting taxonomic treatment. Here, we investigated the taxonomic status of 12 South African root-nodulating Burkholderia isolates from native papilionoid legumes (Hypocalyptus coluteoides, H. oxalidifolius, H. sophoroides and Virgilia oroboides). Analysis of four gene regions (16S rRNA, recA, atpD and rpoB) revealed that the isolates represent a genealogically unique and exclusive assemblage within the genus. Its distinctness was supported by all other aspects of the polyphasic approach utilized, including the genome-based criteria DNA-DNA hybridization (≥70.9%) and average nucleotide identities (≥96%). We accordingly propose the name B. kirstenboschensis sp. nov. for this taxon with isolate Kb15(T) (=LMG 28727(T); =SARC 695(T)) as its type strain. Our data showed that intraspecific genome size differences (≥0.81 Mb) and the occurrence of large DNA regions that are apparently unique to single individuals (16-23% of an isolate's genome) can significantly limit the value of data obtained from DNA-DNA hybridization experiments. Substitution of DNA-DNA hybridization with whole genome sequencing as a prerequisite for the description of Burkholderia species will undoubtedly speed up the pace at which their diversity are documented, especially in hyperdiverse regions such as the Cape Floristic Region. PMID:26472229

  11. Comparison of hup trait and intrinsic antibiotic resistance for assessing rhizobial competitiveness axenically and in soil.

    PubMed

    El Hassan, G A; Hernandez, B S; Focht, D D

    1986-03-01

    The competitiveness of dual-strain inocula of cowpea rhizobia for nodulation of Vigna unguiculata (L.) Walp. was studied axenically between one slow-growing strain (P132, HP147, 401, or 22A1) and one fast-growing strain (176A26 or 176A28) at logarithmic inoculum ratios ranging from 10 to 10. Nodule infectivity was determined by multiple intrinsic antibiotic resistance, since both fast-growing strains were sensitive. Different hydrogen uptake (Hup) efficiencies of dual-strain inocula allowed for the comparison of an indirect rapid method. Infectivity data based on antibiotic resistance and Hup efficiency were fit to linearized fractile plots of log-normal distributions to determine C(AB) (percent infectivity at a 1:1 inoculum density) or I(50) (inoculum ratio at 50% infectivity). The slow growers were always better competitors and had I(50) values which ranged from 7 to 160,000 and C(AB) values which ranged from 62 to 97%. P132 was the best competitor of all those tested. Antibiotic resistance and Hup efficiency methods were in agreement with 401 (Hup) and 176A26 (Hup), but the Hup efficiency method overestimated the I(50) index with 22A1 (Hup) and 176A28 (Hup). The competition of each of the four slow-growing strains with indigenous rhizobia was examined in Cajanus cajan from three tropical soils. Nodule infectivity for all strains ranged from 42 to 96%, and P132 was the best competitor in all the soils. Hup efficiency overestimated infectivity by about 2-fold when Hup inocula (P132 and HP147) were used but underestimated infectivity by more than 100-fold when Hup inocula (401 and 22A1) were used. Although the Hup trait has limited quantitative usage axenically, it is only qualitative in soil competition studies and can only be used with Hup inocula. PMID:16347016

  12. Solitary thyroid nodule. 1. Clinical characteristics

    SciTech Connect

    Mazzaferri, E.L.

    1981-07-01

    The approach to management of an isolated thyroid nodule requires some understanding of the natural history of thyroid cancer and other forms of nodular thyroid disease. The histologic classification of thyroid cancer is an important determinant of survival, as are the size of the primary tumor, presence of thyroid capsule invasion, and presence of distant metastases. Therapeutic radiation and radioactive fallout increase the risk that a thyroid nodule is malignant. Autonomously functioning thyroid nodules are usually benign follicular adenomas and may cause thyrotoxicosis.

  13. Management strategy of solitary pulmonary nodules

    PubMed Central

    Zhan, Ping; Xu, Chunhua; Hao, Keke; Hou, Zhibo; Song, Yong

    2013-01-01

    Solitary pulmonary nodules (SPNs) are increasingly detected with the widespread use of chest computed tomography (CT) scans. The management of patients with SPN should begin with estimating the probability of cancer from the patient’s clinical risk factors and CT characteristics. The decision-making process need to incorporate the probability of cancer, the potential benefits and harms of surgery, the accuracy of the available diagnostic tests and patient preferences. For patients with a very low probability of cancer, careful observation with serial CT is warranted. For patients in the intermediate range of probabilities, either CT-guided fine-needle aspiration biopsy (FNAB) or positron emission tomography (PET), is recommended. For those with a high probability of cancer, surgical diagnosis is warranted. PMID:24409361

  14. Management strategy of solitary pulmonary nodules.

    PubMed

    Zhan, Ping; Xie, Haiyan; Xu, Chunhua; Hao, Keke; Hou, Zhibo; Song, Yong

    2013-12-01

    Solitary pulmonary nodules (SPNs) are increasingly detected with the widespread use of chest computed tomography (CT) scans. The management of patients with SPN should begin with estimating the probability of cancer from the patient's clinical risk factors and CT characteristics. The decision-making process need to incorporate the probability of cancer, the potential benefits and harms of surgery, the accuracy of the available diagnostic tests and patient preferences. For patients with a very low probability of cancer, careful observation with serial CT is warranted. For patients in the intermediate range of probabilities, either CT-guided fine-needle aspiration biopsy (FNAB) or positron emission tomography (PET), is recommended. For those with a high probability of cancer, surgical diagnosis is warranted. PMID:24409361

  15. Radiofrequency ablation of benign thyroid nodules: evaluation of the treatment efficacy using ultrasonography

    PubMed Central

    2016-01-01

    Purpose: The aim of this study was to evaluate the efficacy of radiofrequency (RF) ablation for benign thyroid nodules and assess the usefulness of internal factors (ultrasonographic findings) and external factors (treatment-related findings) in prediction of treatment efficacy. Methods: We evaluated 22 benign thyroid nodules from 19 patients treated with RF ablation between March 2010 and January 2013. The internal and external factors of these nodules were retrospectively reviewed and correlated with the therapeutic success and the volume reduction ratio (VRR). The volume and size of the nodules were determined before treatment, and the VRR was calculated at 6-month and 1-year follow-up examinations after RF ablation. Therapeutic success was defined as a >50% volume reduction. Results: The mean VRRs were 66.1±18.7% at 6 months and 74.3±16.7% at 1 year. The therapeutic success rate after 6 months and 1 year was 81.8% and 90.9%, respectively. At the 1-year follow-up, the margin of the nodule correlated with therapeutic success. Most of the successfully ablated nodules showed well-defined margins on initial ultrasonography (18/20, 90%) (P=0.026). In addition, nodules with ill-defined margins showed a tendency toward having a low VRR at the 6-month and 1-year follow-up examinations. Conclusion: RF ablation was effective in decreasing the volume of benign thyroid nodules. Thyroid nodules with well-defined margins tended to show successful outcomes at the 1-year follow-up examination after RF ablation. PMID:27101983

  16. Effects of Titanium Dioxide Nanoparticles on Red Clover and Its Rhizobial Symbiont.

    PubMed

    Moll, Janine; Okupnik, Annette; Gogos, Alexander; Knauer, Katja; Bucheli, Thomas D; van der Heijden, Marcel G A; Widmer, Franco

    2016-01-01

    Titanium dioxide nanoparticles (TiO2 NPs) are in consideration to be used in plant protection products. Before these products can be placed on the market, ecotoxicological tests have to be performed. In this study, the nitrogen fixing bacterium Rhizobium trifolii and red clover were exposed to two TiO2 NPs, i.e., P25, E171 and a non-nanomaterial TiO2. Growth of both organisms individually and their symbiotic root nodulation were investigated in liquid and hydroponic systems. While 23 and 18 mg l-1 of E171 and non-nanomaterial TiO2 decreased the growth rate of R. trifolii by 43 and 23% respectively, P25 did not cause effects. Shoot length of red clover decreased between 41 and 62% for all tested TiO2 NPs. In 21% of the TiO2 NP treated plants, no nodules were found. At high concentrations certain TiO2 NPs impaired R. trifolii as well as red clover growth and their symbiosis in the hydroponic systems. PMID:27171465

  17. Effects of Titanium Dioxide Nanoparticles on Red Clover and Its Rhizobial Symbiont

    PubMed Central

    Moll, Janine; Okupnik, Annette; Gogos, Alexander; Knauer, Katja; Bucheli, Thomas D.; van der Heijden, Marcel G. A.; Widmer, Franco

    2016-01-01

    Titanium dioxide nanoparticles (TiO2 NPs) are in consideration to be used in plant protection products. Before these products can be placed on the market, ecotoxicological tests have to be performed. In this study, the nitrogen fixing bacterium Rhizobium trifolii and red clover were exposed to two TiO2 NPs, i.e., P25, E171 and a non-nanomaterial TiO2. Growth of both organisms individually and their symbiotic root nodulation were investigated in liquid and hydroponic systems. While 23 and 18 mg l-1 of E171 and non-nanomaterial TiO2 decreased the growth rate of R. trifolii by 43 and 23% respectively, P25 did not cause effects. Shoot length of red clover decreased between 41 and 62% for all tested TiO2 NPs. In 21% of the TiO2 NP treated plants, no nodules were found. At high concentrations certain TiO2 NPs impaired R. trifolii as well as red clover growth and their symbiosis in the hydroponic systems. PMID:27171465

  18. Mechanisms of nodule-specific melanization in the hemocoel of the silkworm, Bombyx mori.

    PubMed

    Shu, Min; Mang, Dingze; Fu, Gege Sun; Tanaka, Shiho; Endo, Haruka; Kikuta, Shingo; Sato, Ryoichi

    2016-03-01

    In the insect immune system, nodules are known to be a product of the cellular response against microorganisms and may be a preferential target for melanization. However, the mechanism of nodule-preferential melanization remains to be explored. In this study, we identified several mechanisms of nodule-preferential melanization by analyzing congregation and the activation of several factors involved in the prophenoloxidase (proPO)-activating system in the silkworm, Bombyx mori. Microorganism-binding assays revealed that B. mori larval plasma have an effective invading microorganism-surveillance network consisting of at least six pattern-recognition receptors (PRRs). We also found that a hemolymph serine proteinase, BmHP14, can bind to Saccharomyces cerevisiae. Pull-down assays showed that PRR C-type lectins form protein complexes with serine proteinase homologs, BmSPH1 and BmSPH2, which leads to the activated forms of BmSPH1 and BmSPH2 being gathered on microorganisms and trapped in nodules. Immunostaining analysis revealed that most factors in the proPO-activating system and some factors in the triggering system for antimicrobial peptide production exist in the granules of hemocytes which can gather in nodules. Western blot analysis showed that factors in the proPO-activating system are congregated in formed nodules by their concentration in plasma and aggregating hemocytes. PMID:26707571

  19. Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus.

    PubMed

    De Luis, Ana; Markmann, Katharina; Cognat, Valérie; Holt, Dennis B; Charpentier, Myriam; Parniske, Martin; Stougaard, Jens; Voinnet, Olivier

    2012-12-01

    Legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. Nodule development involves the distinct processes of nodule organogenesis, bacterial infection, and the onset of nitrogen fixation. These entail profound, dynamic gene expression changes, notably contributed to by microRNAs (miRNAs). Here, we used deep-sequencing, candidate-based expression studies and a selection of Lotus japonicus mutants uncoupling different symbiosis stages to identify miRNAs involved in symbiotic nitrogen fixation. Induction of a noncanonical miR171 isoform, which targets the key nodulation transcription factor Nodulation Signaling Pathway2, correlates with bacterial infection in nodules. A second candidate, miR397, is systemically induced in the presence of active, nitrogen-fixing nodules but not in that of noninfected or inactive nodule organs. It is involved in nitrogen fixation-related copper homeostasis and targets a member of the laccase copper protein family. These findings thus identify two miRNAs specifically responding to symbiotic infection and nodule function in legumes. PMID:23071252

  20. Sulphasalazine and regression of rheumatoid nodules.

    PubMed

    Englert, H J; Hughes, G R; Walport, M J

    1987-03-01

    The regression of small rheumatoid nodules was noted in four patients after starting sulphasalazine therapy. This coincided with an improvement in synovitis and also falls in erythrocyte sedimentation rate (ESR) and C reactive protein (CRP). The relation between the nodule regression and the sulphasalazine therapy is discussed. PMID:2883940

  1. Simulating nodules in chest radiographs with real nodules from multi-slice CT images

    NASA Astrophysics Data System (ADS)

    Schilham, Arnold; van Ginneken, Bram

    2006-03-01

    To improve the detection of nodules in chest radiographs, large databases of chest radiographs with annotated, proven nodules are needed for training of both radiologists and computer-aided detection systems. The construction of such databases is a laborious and time-consuming task. This study presents a novel technique to produce large amounts of chest x-rays with annotated, simulated nodules. Realistic nodules in radiographs are generated using real nodules segmented from CT images. Results from an observer study indicate that the simulated nodules can not be distinguished from real nodules. This method has great potential to aid the development of automated detection systems and to generate teaching files for human observers.

  2. Rheumatoid nodule presenting as Morton's neuroma.

    PubMed

    Chaganti, S; Joshy, S; Hariharan, K; Rashid, M

    2013-09-01

    Among 101 feet that presented with symptoms and signs similar to Morton's neuroma, intermetatarsal rheumatoid nodules were found in five feet (three patients). Two patients had bilateral involvement. Histology of the excised tissue showed the presence of a rheumatoid nodule and Morton's neuroma in four feet and a rheumatoid nodule with unremarkable nerve bundles in one. A rheumatoid nodule can coexist with Morton's neuroma, as seen in our patients, and the presentation is often similar to that of a Morton's neuroma. Our patients were rendered asymptomatic with surgical treatment and went on to have appropriate management of rheumatoid arthritis. Rheumatoid nodule should be considered in the differential diagnosis of Morton's neuroma in not only rheumatoid arthritis patients but also asymptomatic patients who have never been tested for rheumatoid antibodies. PMID:23135058

  3. Cytopathology of Follicular Cell Nodules.

    PubMed

    Damiani, Domenico; Suciu, Voichita; Vielh, Philippe

    2015-12-01

    This article corresponds to a lecture delivered during the Endocrine Pathology Society symposium held in Boston on 21 March 2015 (104th USCAP meeting, March 21-27). It focuses on the importance of cytopathology in endocrine thyroid pathology and the limits and pitfalls of diagnosis in follicular cell lesions. Lights and shadows are present in each diagnostic technique: Fine needle aspiration has imposed itself as a gold standard in thyroid nodules thanks to its easiness of execution and high cost-effectiveness ratio. A milestone in this field is represented by the National Cancer Institute (NCI) Thyroid Fine Needle Aspiration (FNA) State of the State of the Science Conference hosted in October 22-23, 2007 by the NCI, followed by a series of documents published in Diagnostic Cytopathology and Cytojournal (2008) as well as in an atlas entitled: The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC): terminology and criteria (2010, Springer). "Gray" zones still remain, causing difficulties and anxiety to the cytopathologist when facing challenging cases. Each diagnostic category of TBSRTC is analyzed and discussed in a concise fashion with special emphasis on challenging cases such as atypia of undetermined significance (AUS), suspicion for follicular neoplasms (SFNs), diagnoses of papillary thyroid carcinoma (PTC) in Hashimoto thyroiditis and follicular variant of papillary carcinoma (FVPTC). Our aim was to better define and clarify the spectrum of follicular cell lesions in thyroid nodule samplings and to underline the diagnostic limits in order to avoid pitfalls. New emerging molecular biology techniques may represent useful tools in selected morphological challenging cases and lead to new therapeutic approaches in line with drug-tailored therapy and personalized medicine. PMID:26227345

  4. Influence of Nodule Detection Software on Radiologists’ Confidence in Identifying Pulmonary Nodules With Computed Tomography

    PubMed Central

    Nietert, Paul J.; Ravenel, James G.; Taylor, Katherine K.; Silvestri, Gerard A.

    2011-01-01

    Purpose With advances in technology, detection of small pulmonary nodules is increasing. Nodule detection software (NDS) has been developed to assist radiologists with pulmonary nodule diagnosis. Although it may increase sensitivity for small nodules, often there is an accompanying increase in false-positive findings. We designed a study to examine the extent to which computed tomography (CT) NDS influences the confidence of radiologists in identifying small pulmonary nodules. Materials and Methods Eight radiologists (readers) with different levels of experience examined thoracic CT scans of 131 cases and identified all the clinically relevant pulmonary nodules. The reference standard was established by an expert, dedicated thoracic radiologist. For each nodule, the readers recorded nodule size, density, location, and confidence level. Two weeks (or more) later, the readers reinterpreted the same scans; however, this time they were provided marks, when present, as indicated by NDS and asked to reassess their level of confidence. The effect of NDS on changes in reader confidence was assessed using multivariable generalized linear regression models. Results A total of 327 unique nodules were identified. Declines in confidence were significantly (P<0.05) associated with the absence of an NDS mark and smaller nodules (odds ratio=71.0, 95% confidence interval =14.8–339.7). Among nodules with pre-NDS confidence less than 100%, increases in confidence were significantly (P<0.05) associated with the presence of an NDS mark (odds ratio=6.0, 95% confidence interval =2.7–13.6) and larger nodules. Secondary findings showed that NDS did not improve reader diagnostic accuracy. Conclusion Although in this study NDS does not seem to enhance reader accuracy, the confidence of the radiologists in identifying small pulmonary nodules with CT is greatly influenced by NDS. PMID:20498624

  5. Aspartate Aminotransferase in Alfalfa Root Nodules 1

    PubMed Central

    Farnham, Mark W.; Griffith, Stephen M.; Miller, Susan S.; Vance, Carroll P.

    1990-01-01

    Aspartate aminotransferase (AAT) plays an important role in nitrogen metabolism in all plants and is particularly important in the assimilation of fixed N derived from the legume-Rhizoblum symbiosis. Two isozymes of AAT (AAT-1 and AAT-2) occur in alfalfa (Medicago sativa L.). Antibodies against alfalfa nodule AAT-2 do not recognize AAT-1, and these antibodies were used to study AAT-2 expression in different tissues and genotypes of alfalfa and also in other legume and nonlegume species. Rocket immunoelectrophoresis indicated that nodules of 38-day-old alfalfa plants contained about eight times more AAT-2 than did nodules of 7-day-old plants, confirming the nodule-enhanced nature of this isozyme. AAT-2 was estimated to make up 16, 15, 5, and 8 milligrams per gram of total soluble protein in mature nodules, roots, stems, and leaves, respectively, of effective N2-fixing alfalfa. The concentration of AAT-2 in nodules of ineffective non-N2-fixing alafalfa genotypes was about 70% less than that of effective nodules. Western blots of soluble protein from nodules of nine legume species indicated that a 40-kilodalton polypeptide that reacts strongly with AAT-2 antibodies is conserved in legumes. Nodule AAT-2 immunoprecipitation data suggested that amide- and ureide-type legumes may differ in expression and regulation of the enzyme. In addition, Western blotting and immunoprecipitations of AAT activity demonstrated that antibodies against alfalfa AAT-2 are highly cross-reactive with AAT enzyme protein in leaves of soybean (Glycine max L.), wheat (Triticum aestivum L.), and maize (Zea mays L.) and in roots of maize, but not with AAT in soybean and wheat roots. Results from this study indicate that AAT-2 is structurally conserved and localized in similar tissues among diverse species. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:16667896

  6. Oxidation state of marine manganese nodules

    USGS Publications Warehouse

    Piper, D.Z.; Basler, J.R.; Bischoff, J.L.

    1984-01-01

    Analyses of the bulk oxidation state of marine manganese nodules indicates that more than 98% of the Mn in deep ocean nodules is present as Mn(IV). The samples were collected from three quite different areas: the hemipelagic environment of the Guatemala Basin, the pelagic area of the North Pacific, and seamounts in the central Pacific. Results of the study suggest that todorokite in marine nodules is fully oxidized and has the following stoichiometry: (K, Na, Ca, Ba).33(Mg, Cu, Ni).76Mn5O22(H2O)3.2. ?? 1984.

  7. Relationship of anthropometric measurements to thyroid nodules in a Chinese population

    PubMed Central

    Xu, Weimin; Chen, Zexin; Li, Na; Liu, Hui; Huo, Liangliang; Huang, Yangmei; Jin, Xingyi; Deng, Jin; Zhu, Sujuan; Zhang, Shanchun; Yu, Yunxian

    2015-01-01

    Objective Previous studies have found that overweight and obesity are related to numerous diseases, including thyroid cancer and thyroid volume. This study evaluates the relationship between body size and the presence of thyroid nodules in a Chinese population. Methods A total of 6793 adults and 2410 children who underwent thyroid ultrasonography were recruited in this cross-sectional study in Hangzhou, Zhejiang Province, China, from March to October, 2010. Sociodemographic characteristics and potential risk factors of thyroid nodules were collected by questionnaire. Height and weight were measured using standard protocols. Associations of height, weight, body mass index (BMI) and body surface area (BSA) with the presence of thyroid nodules were evaluated using multiple logistic regression models. Results After adjustment for potential risk factors, an increased risk of thyroid nodule incidence was associated with height (OR 1.15, 95% CI 1.02 to 1.30), weight (OR 1.40, 95% CI 1.24 to 1.58), BMI (OR 1.26, 95% CI 1.11 to 1.42) and BSA (OR 1.43, 95% CI 1.27 to 1.62) in all adults, but most obviously in women. In children, similar associations were observed between risk of thyroid nodule incidence and weight, BMI and BSA, but not height. BSA was the measurement most significantly associated with thyroid nodules in both adults and children. Conclusions This study identified that the presence of thyroid nodules was positively associated with weight, height, BMI and BSA in both women and girls. It suggests that tall, obese individuals have increased susceptibility to thyroid nodules. Trial registration number: NCT01838629. PMID:26692553

  8. Ribotyping of rhizobia nodulating Acacia mangium and Paraserianthes falcataria from different geographical areas in Indonesia using PCR-RFLP-SSCP (PRS) and sequencing.

    PubMed

    Clapp, J P; Mansur, I; Dodd, J C; Jeffries, P

    2001-04-01

    Acacia mangium and Paraserianthes falcataria are leguminous tree species widely grown for timber in Indonesia and other tropical countries, yet little is known about the identity of their rhizobial symbionts. Polymerase chain reaction-restriction fragment length polymorphism-single-strand conformational polymorphism (PRS) analysis of the 16S rRNA gene was used along with sequencing to assess the diversity of 57 rhizobia isolated from nodules of A. mangium and P. falctaria in Indonesia. In total, 26 rhizobia isolated from A. mangium were analysed by PRS and sequencing. The PRS patterns indicated that 12 (46%) clustered with Bradyrhizobium elkanii, 13 (50%) with B. lianoningense/japonicum and one (4%) with Mesorhizobium loti. Thirty-one isolates were analysed from P. falcataria: five (16%) clustered with B. elkanii and 26 (84%) with B. lianoningense/japonicum. These results were confirmed by phylogenetic analysis of sequences. Intraspecific diversity of the 16S rRNA genes from rhizobia nodulating A. mangium and P. falcataria revealed by PRS was low, only one genotype was found within the isolates that clustered with B. elkanii and two within the B. liaoningense/japonicum group. These Bradyrhizobium species are apparently ubiquitous throughout the Indonesian archipelago and it is clear why the two tree species are able to successfully establish outside their native range without the need for inoculation with indigenous rhizobia. PMID:11359513

  9. The Small GTPase ROP10 of Medicago truncatula Is Required for Both Tip Growth of Root Hairs and Nod Factor-Induced Root Hair Deformation

    PubMed Central

    Lei, Ming-Juan; Wang, Qi; Li, Xiaolin; Chen, Aimin; Luo, Li; Xie, Yajun; Li, Guan; Luo, Da; Mysore, Kirankumar S.; Wen, Jiangqi; Xie, Zhi-Ping; Staehelin, Christian; Wang, Yan-Zhang

    2015-01-01

    Rhizobia preferentially enter legume root hairs via infection threads, after which root hairs undergo tip swelling, branching, and curling. However, the mechanisms underlying such root hair deformation are poorly understood. Here, we showed that a type II small GTPase, ROP10, of Medicago truncatula is localized at the plasma membrane (PM) of root hair tips to regulate root hair tip growth. Overexpression of ROP10 and a constitutively active mutant (ROP10CA) generated depolarized growth of root hairs, whereas a dominant negative mutant (ROP10DN) inhibited root hair elongation. Inoculated with Sinorhizobium meliloti, the depolarized swollen and ballooning root hairs exhibited extensive root hair deformation and aberrant infection symptoms. Upon treatment with rhizobia-secreted nodulation factors (NFs), ROP10 was transiently upregulated in root hairs, and ROP10 fused to green fluorescent protein was ectopically localized at the PM of NF-induced outgrowths and curls around rhizobia. ROP10 interacted with the kinase domain of the NF receptor NFP in a GTP-dependent manner. Moreover, NF-induced expression of the early nodulin gene ENOD11 was enhanced by the overexpression of ROP10 and ROP10CA. These data suggest that NFs spatiotemporally regulate ROP10 localization and activity at the PM of root hair tips and that interactions between ROP10 and NF receptors are required for root hair deformation and continuous curling during rhizobial infection. PMID:25794934

  10. The small GTPase ROP10 of Medicago truncatula is required for both tip growth of root hairs and nod factor-induced root hair deformation.

    PubMed

    Lei, Ming-Juan; Wang, Qi; Li, Xiaolin; Chen, Aimin; Luo, Li; Xie, Yajun; Li, Guan; Luo, Da; Mysore, Kirankumar S; Wen, Jiangqi; Xie, Zhi-Ping; Staehelin, Christian; Wang, Yan-Zhang

    2015-03-01

    Rhizobia preferentially enter legume root hairs via infection threads, after which root hairs undergo tip swelling, branching, and curling. However, the mechanisms underlying such root hair deformation are poorly understood. Here, we showed that a type II small GTPase, ROP10, of Medicago truncatula is localized at the plasma membrane (PM) of root hair tips to regulate root hair tip growth. Overexpression of ROP10 and a constitutively active mutant (ROP10CA) generated depolarized growth of root hairs, whereas a dominant negative mutant (ROP10DN) inhibited root hair elongation. Inoculated with Sinorhizobium meliloti, the depolarized swollen and ballooning root hairs exhibited extensive root hair deformation and aberrant infection symptoms. Upon treatment with rhizobia-secreted nodulation factors (NFs), ROP10 was transiently upregulated in root hairs, and ROP10 fused to green fluorescent protein was ectopically localized at the PM of NF-induced outgrowths and curls around rhizobia. ROP10 interacted with the kinase domain of the NF receptor NFP in a GTP-dependent manner. Moreover, NF-induced expression of the early nodulin gene ENOD11 was enhanced by the overexpression of ROP10 and ROP10CA. These data suggest that NFs spatiotemporally regulate ROP10 localization and activity at the PM of root hair tips and that interactions between ROP10 and NF receptors are required for root hair deformation and continuous curling during rhizobial infection. PMID:25794934

  11. Unusual Methyl-Branched α,β-Unsaturated Acyl Chain Substitutions in the Nod Factors of an Arctic Rhizobium, Mesorhizobium sp. Strain N33 (Oxytropis arctobia)

    PubMed Central

    Poinsot, Véréna; Bélanger, Elaine; Laberge, Serge; Yang, Guo-Ping; Antoun, Hani; Cloutier, Jean; Treilhou, Michel; Dénarié, Jean; Promé, Jean-Claude; Debellé, Frédéric

    2001-01-01

    Mesorhizobium sp. strain N33 (Oxytropis arctobia), a rhizobial strain isolated in arctic Canada, is able to fix nitrogen at very low temperatures in association with a few arctic legume species belonging to the genera Astragalus, Onobrychis, and Oxytropis. Using mass spectrometry and nuclear magnetic resonance spectroscopy, we have determined the structure of N33 Nod factors, which are major determinants of nodulation. They are pentameric lipochito-oligosaccharides 6-O sulfated at the reducing end and exhibit other original substitutions: 6-O acetylation of the glucosamine residue next to the nonreducing terminal glucosamine and N acylation of the nonreducing terminal glucosamine by methyl-branched acyl chains of the iso series, some of which are α,β unsaturated. These unusual substitutions may contribute to the peculiar host range of N33. Analysis of N33 whole-cell fatty acids indicated that synthesis of the methyl-branched fatty acids depended on the induction of bacteria by plant flavonoids, suggesting a specific role for these fatty acids in the signaling process between the plant and the bacteria. Synthesis of the methyl-branched α,β-unsaturated fatty acids required a functional nodE gene. PMID:11371536

  12. [Benign thyroid nodules: diagnostic and therapeutic approach].

    PubMed

    Durante, Cosimo; Cava, Francesco; Paciaroni, Alessandra; Filetti, Sebastiano

    2008-05-01

    In the last years an increase in thyroid nodules detection has been reported from several epidemiological studies. This trend is largely due to the routine use of diagnostic sonography procedures in clinical practice. Thyroid nodules, both palpable or not palpable, rarely turn out to be malignant. Fine-needle aspiration cytology (FNAc) plays a central role in establishing the nature of the nodule. Excluded the presence of malignant lesions, which are generally treated with surgery, physicians are faced with a variety of therapeutic options, and choosing the optimal approach can be a difficult task. These include a periodic follow-up alone without treatment, the iodine supplementation, the thyroid-hormone suppressive therapy, the radioiodine administration, the percutaneous ethanol injections, and the new technique of laser photocoagulation. In all cases, decisions on the management of benign thyroid nodules should always be based on clinical target and a careful analysis of benefits and risks to the patient. PMID:18581970

  13. Nitrate inhibition of legume nodule growth and activity. I. Long term studies with a continuous supply of nitrate

    SciTech Connect

    Streeter, J.G.

    1985-02-01

    The synthesis and accumulation of nitrite has been suggested as a causative factor in the inhibition of legume nodules supplied with nitrate. Plants were grown in sand culture with a moderate level of nitrate (2.1 to 6.4 millimolar) supplied continuously from seed germination to 30 to 50 days after planting. In a comparison of nitrate treatments, a highly significant negative correlation between nitrite concentration in soybean (Glycine max (L.) Merr.) nodules and nodule fresh weight per shoot dry weight was found even when bacteroids lacked nitrate reductase (NR). However, in a comparison of two Rhizobium japonicum strains, there was only 12% as much nitrite in nodules formed by NR/sup -/ R. japonicum as in nodules formed by NR/sup +/ R. japonicum, and growth and acetylene reduction activity of both types of nodules was about equally inhibited. The very small concentration of nitrite found in P. vulgaris nodules was probably below that required for the inhibition of nitrogenase based on published in vitro experiments, and yet the specific acetylene reduction activity was inhibited 83% by nitrate. The overall results do not support the idea that nitrite plays a role in the inhibition of nodule growth and nitrogenase activity by nitrate.

  14. Incidentally diagnosed pulmonary nodule: a diagnostic algorithm

    PubMed Central

    Rzyman, Witold

    2014-01-01

    Asymptomatic solitary pulmonary nodules incidentally revealed by computed tomography has become a serious medical problem. Depending on their diameter, solid, part-solid, or pure ground-glass pulmonary nodules may be observed, diagnosed radiologically/invasively, or resected in accordance with international guidelines. Pure ground-glass nodules, semi-solid lesions, or solid lesions smaller than 8 mm should be monitored by serial low-dose computed tomography. In the case of solid nodules greater than 8 mm, the assessment of the risk of malignancy is recommended. Patients at high risk of lung cancer with pulmonary lesions should undergo diagnostic investigation, or the nodule should be resected. If the risk of lung cancer is low, the patients may be monitored. Needle aspiration biopsy is the most important invasive method of tumor diagnosis. Cytological or histopathological diagnosis is helpful in appropriate clinical decision making that reduces the risk of unnecessary surgery, decreasing the rate of benign nodule resections and thus reducing the costs of medical treatment. PMID:26336456

  15. Incidental thyroid nodules and thyroid cancer: considerations before determining management.

    PubMed

    Tufano, Ralph P; Noureldine, Salem I; Angelos, Peter

    2015-06-01

    The worldwide incidence of thyroid cancer is increasing substantially, almost exclusively attributable to small papillary thyroid cancers. Increased use of diagnostic imaging is considered the most likely explanation for this reported rise, but other factors may also be contributing. The increase in health care expenditures related to managing these presumably low-risk cancers, without a clear patient benefit, has resulted in a backlash against the early detection of thyroid cancer. Currently, there is no way to confidently predict which incidentally detected thyroid nodule may be the precursor to a more aggressive process. Predictions such as these would require more accurate characterization of the biology of individual thyroid cancers than is currently possible. With time, we might prove our ability to confidently differentiate low-risk from high-risk thyroid cancers, but until that happens, routine screening for thyroid cancer by imaging billed as a "health checkup" should not be performed. However, incidentally detected thyroid nodules should be reported, and a clear medical team management plan should be developed. Our ethical responsibility is to provide patients with objective, evidence-based information about their disease status, not to assume that we know what is best for them by selectively withholding information. In addition, providing patients with psychosocial assistance will help them process the information necessary to make informed decisions that will provide them with the most value when a small thyroid nodule or cancer is incidentally identified. Herein, we summarize the epidemiological data for disease incidence, discuss some controversies in disease management, and outline the key elements and ethical considerations of informed decision making as they apply to managing incidentally detected thyroid nodules and thyroid cancer. PMID:25928353

  16. Microsymbiont diversity and phylogeny of native bradyrhizobia associated with soybean (Glycine max L. Merr.) nodulation in South African soils.

    PubMed

    Naamala, Judith; Jaiswal, Sanjay K; Dakora, Felix D

    2016-07-01

    The genetic diversity and identification of slow- and fast-growing soybean root nodule bacterial isolates from different agro-climatic regions in Mpumalanga, Limpopo and Gauteng Provinces of South Africa were evaluated. The 16S-rDNA-RFLP analysis of 100 rhizobial isolates and eight reference type strains placed the isolates into six major clusters, and revealed their site-dependent genomic diversity. Sequence analysis of single and concatenated housekeeping genes (atpD, glnII and gyrB), as well as the symbiotic gene nifH captured a considerably higher level of genetic diversity and indicated the dominance of Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum in Mpumalanga, Limpopo and Gauteng Provinces. Gene sequence similarities of isolates with type strains of Bradyrhizobium ranged from 97.3 to 100% for the 16S rDNA, and 83.4 to 100% for the housekeeping genes. The glnII gene phylogeny showed discordance with the other genes, suggesting lateral gene transfer or recombination events. Concatenated gene sequence analysis showed that most of the isolates did not align with known type strains and might represent new species from South Africa. This underscores the high genetic variability associated with soybean Bradyrhizobium in South African soils, and the presence of an important reservoir of novel soybean-nodulating bradyrhizobia in the country. In this study, the grouping of isolates was influenced by site origin, with Group I isolates originating from Limpopo Province and Groups II and III from Mpumlanga Province in the 16S rDNA-RFLP analysis. PMID:27324571

  17. Functional analysis of duplicated Symbiosis Receptor Kinase (SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max).

    PubMed

    Indrasumunar, Arief; Wilde, Julia; Hayashi, Satomi; Li, Dongxue; Gresshoff, Peter M

    2015-03-15

    Association between legumes and rhizobia results in the formation of root nodules, where symbiotic nitrogen fixation occurs. The early stages of this association involve a complex of signalling events between the host and microsymbiont. Several genes dealing with early signal transduction have been cloned, and one of them encodes the leucine-rich repeat (LRR) receptor kinase (SymRK; also termed NORK). The Symbiosis Receptor Kinase gene is required by legumes to establish a root endosymbiosis with Rhizobium bacteria as well as mycorrhizal fungi. Using degenerate primer and BAC sequencing, we cloned duplicated SymRK homeologues in soybean called GmSymRKα and GmSymRKβ. These duplicated genes have high similarity of nucleotide (96%) and amino acid sequence (95%). Sequence analysis predicted a malectin-like domain within the extracellular domain of both genes. Several putative cis-acting elements were found in promoter regions of GmSymRKα and GmSymRKβ, suggesting a participation in lateral root development, cell division and peribacteroid membrane formation. The mutant of SymRK genes is not available in soybean; therefore, to know the functions of these genes, RNA interference (RNAi) of these duplicated genes was performed. For this purpose, RNAi construct of each gene was generated and introduced into the soybean genome by Agrobacterium rhizogenes-mediated hairy root transformation. RNAi of GmSymRKβ gene resulted in an increased reduction of nodulation and mycorrhizal infection than RNAi of GmSymRKα, suggesting it has the major activity of the duplicated gene pair. The results from the important crop legume soybean confirm the joint phenotypic action of GmSymRK genes in both mycorrhizal and rhizobial infection seen in model legumes. PMID:25617765

  18. Investigation of lung nodule detectability in low-dose 320-slice computed tomography

    PubMed Central

    Silverman, J. D.; Paul, N. S.; Siewerdsen, J. H.

    2009-01-01

    Low-dose imaging protocols in chest CT are important in the screening and surveillance of suspicious and indeterminate lung nodules. Techniques that maintain nodule detectability yet permit dose reduction, particularly for large body habitus, were investigated. The objective of this study was to determine the extent to which radiation dose can be minimized while maintaining diagnostic performance through knowledgeable selection of reconstruction techniques. A 320-slice volumetric CT scanner (Aquilion ONE™, Toshiba Medical Systems) was used to scan an anthropomorphic phantom at doses ranging from ∼0.1 mGy up to that typical of low-dose CT (LDCT, ∼5 mGy) and diagnostic CT (∼10 mGy). Radiation dose was measured via Farmer chamber and MOSFET dosimetry. The phantom presented simulated nodules of varying size and contrast within a heterogeneous background, and chest thickness was varied through addition of tissue-equivalent bolus about the chest. Detectability of a small solid lung nodule (3.2 mm diameter, −37 HU, typically the smallest nodule of clinical significance in screening and surveillance) was evaluated as a function of dose, patient size, reconstruction filter, and slice thickness by means of nine-alternative forced-choice (9AFC) observer tests to quantify nodule detectability. For a given reconstruction filter, nodule detectability decreased sharply below a threshold dose level due to increased image noise, especially for large body size. However, nodule detectability could be maintained at lower doses through knowledgeable selection of (smoother) reconstruction filters. For large body habitus, optimal filter selection reduced the dose required for nodule detection by up to a factor of ∼3 (from ∼3.3 mGy for sharp filters to ∼1.0 mGy for the optimal filter). The results indicate that radiation dose can be reduced below the current low-dose (5 mGy) and ultralow-dose (1 mGy) levels with knowledgeable selection of reconstruction parameters. Image

  19. Automatic two-step detection of pulmonary nodules

    NASA Astrophysics Data System (ADS)

    Dolejší, Martin; Kybic, Jan

    2007-03-01

    We present a computer-aided diagnosis (CAD) system to detect small-size (from 2mm to around 10mm) pulmonary nodules from helical CT scans. A pulmonary nodule is a small, round (parenchymal nodule) or worm (juxta-pleural) shaped lesion in the lungs. Both have greater radio density than lungs parenchyma. Lung nodules may indicate a lung cancer and its detection in early stage improves survival rate of patients. CT is considered to be the most accurate imaging modality for detection of nodules. However, the large amount of data per examination makes the interpretation difficult. This leads to omission of nodules by human radiologist. CAD system presented is designed to help lower the number of omissions. Our system uses two different schemes to locate juxtapleural nodules and parenchymal nodules. For juxtapleural nodules, morphological closing and thresholding is used to find nodule candidates. To locate non-pleural nodule candidates, 3D blob detector uses multiscale filtration. Ellipsoid model is fitted on nodules. To define which of the nodule candidates are in fact nodules, an additional classification step is applied. Linear and multi-threshold classifiers are used. System was tested on 18 cases (4853 slices) with total sensitivity of 96%, with about 12 false positives/slice. The classification step reduces number of false positives to 9 per slice without significantly decreasing sensitivity (89,6%).

  20. Enhanced CT images by the wavelet transform improving diagnostic accuracy of chest nodules.

    PubMed

    Guo, Xiuhua; Liu, Xiangye; Wang, Huan; Liang, Zhigang; Wu, Wei; He, Qian; Li, Kuncheng; Wang, Wei

    2011-02-01

    The objective of this study was to compare the diagnostic accuracy in the interpretation of chest nodules using original CT images versus enhanced CT images based on the wavelet transform. The CT images of 118 patients with cancers and 60 with benign nodules were used in this study. All images were enhanced through an algorithm based on the wavelet transform. Two experienced radiologists interpreted all the images in two reading sessions. The reading sessions were separated by a minimum of 1 month in order to minimize the effect of observer's recall. The Mann-Whitney U nonparametric test was used to analyze the interpretation results between original and enhanced images. The Kruskal-Wallis H nonparametric test of K independent samples was used to investigate the related factors which could affect the diagnostic accuracy of observers. The area under the ROC curves for the original and enhanced images was 0.681 and 0.736, respectively. There is significant difference in diagnosing the malignant nodules between the original and enhanced images (z = 7.122, P < 0.001), whereas there is no significant difference in diagnosing the benign nodules (z = 0.894, P = 0.371). The results showed that there is significant difference between original and enhancement images when the size of nodules was larger than 2 cm (Z = -2.509, P = 0.012, indicating the size of the nodules is a critical evaluating factor of the diagnostic accuracy of observers). This study indicated that the image enhancement based on wavelet transform could improve the diagnostic accuracy of radiologists for the malignant chest nodules. PMID:19937084

  1. Wuschel-related homeobox5 gene expression and interaction of CLE peptides with components of the systemic control add two pieces to the puzzle of autoregulation of nodulation.

    PubMed

    Osipova, Maria A; Mortier, Virginie; Demchenko, Kirill N; Tsyganov, Victor E; Tikhonovich, Igor A; Lutova, Ludmila A; Dolgikh, Elena A; Goormachtig, Sofie

    2012-03-01

    In legumes, the symbiotic nodules are formed as a result of dedifferentiation and reactivation of cortical root cells. A shoot-acting receptor complex, similar to the Arabidopsis (Arabidopsis thaliana) CLAVATA1 (CLV1)/CLV2 receptor, regulating development of the shoot apical meristem, is involved in autoregulation of nodulation (AON), a mechanism that systemically controls nodule number. The targets of CLV1/CLV2 in the shoot apical meristem, the WUSCHEL (WUS)-RELATED HOMEOBOX (WOX) family transcription factors, have been proposed to be important regulators of apical meristem maintenance and to be expressed in apical meristem "organizers." Here, we focus on the role of the WOX5 transcription factor upon nodulation in Medicago truncatula and pea (Pisum sativum) that form indeterminate nodules. Analysis of temporal WOX5 expression during nodulation with quantitative reverse transcription-polymerase chain reaction and promoter-reporter fusion revealed that the WOX5 gene was expressed during nodule organogenesis, suggesting that WOX genes are common regulators of cell proliferation in different systems. Furthermore, in nodules of supernodulating mutants, defective in AON, WOX5 expression was higher than that in wild-type nodules. Hence, a conserved WUS/WOX-CLV regulatory system might control cell proliferation and differentiation not only in the root and shoot apical meristems but also in nodule meristems. In addition, the link between nodule-derived CLE peptides activating AON in different legumes and components of the AON system was investigated. We demonstrate that the identified AON component, NODULATION3 of pea, might act downstream from or beside the CLE peptides during AON. PMID:22232385

  2. Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses

    PubMed Central

    Tromas, Alexandre; Parizot, Boris; Diagne, Nathalie; Champion, Antony; Hocher, Valérie; Cissoko, Maïmouna; Crabos, Amandine; Prodjinoto, Hermann; Lahouze, Benoit; Bogusz, Didier; Laplaze, Laurent; Svistoonoff, Sergio

    2012-01-01

    To improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. A few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. Fossil and molecular data suggest that the molecular mechanisms involved in these root nodule symbioses (RNS) have been partially recycled from more ancient and widespread arbuscular mycorrhizal (AM) symbiosis. We used a comparative transcriptomics approach to identify genes involved in establishing these 3 endosymbioses and their functioning. We analysed global changes in gene expression in AM in the actinorhizal tree C. glauca. A comparison with genes induced in AM in Medicago truncatula and Oryza sativa revealed a common set of genes induced in AM. A comparison with genes induced in nitrogen-fixing nodules of C. glauca and M. truncatula also made it possible to define a common set of genes induced in these three endosymbioses. The existence of this core set of genes is in accordance with the proposed recycling of ancient AM genes for new functions related to nodulation in legumes and actinorhizal plants. PMID:22970303

  3. Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season.

    PubMed

    Siczek, Anna; Lipiec, Jerzy

    2016-01-01

    Inoculation of legume seeds with Rhizobium affects soil microbial community and processes, especially in the rhizosphere. This study aimed at assessing the effect of Rhizobium inoculation on microbial activity in the faba bean rhizosphere during the growing season in a field experiment on a Haplic Luvisol derived from loess. Faba bean (Vicia faba L.) seeds were non-inoculated (NI) or inoculated (I) with Rhizobium leguminosarum bv. viciae and sown. The rhizosphere soil was analyzed for the enzymatic activities of dehydrogenases, urease, protease and acid phosphomonoesterase, and functional diversity (catabolic potential) using the Average Well Color Development, Shannon-Weaver, and Richness indices following the community level physiological profiling from Biolog EcoPlate™. The analyses were done on three occasions corresponding to the growth stages of: 5-6 leaf, flowering, and pod formation. The enzymatic activities were higher in I than NI (p < 0.05) throughout the growing season. However, none of the functional diversity indices differed significantly under both treatments, regardless of the growth stage. This work showed that the functional diversity of the microbial communities was a less sensitive tool than enzyme activities in assessment of rhizobial inoculation effects on rhizosphere microbial activity. PMID:27213363

  4. Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season

    PubMed Central

    Siczek, Anna; Lipiec, Jerzy

    2016-01-01

    Inoculation of legume seeds with Rhizobium affects soil microbial community and processes, especially in the rhizosphere. This study aimed at assessing the effect of Rhizobium inoculation on microbial activity in the faba bean rhizosphere during the growing season in a field experiment on a Haplic Luvisol derived from loess. Faba bean (Vicia faba L.) seeds were non-inoculated (NI) or inoculated (I) with Rhizobium leguminosarum bv. viciae and sown. The rhizosphere soil was analyzed for the enzymatic activities of dehydrogenases, urease, protease and acid phosphomonoesterase, and functional diversity (catabolic potential) using the Average Well Color Development, Shannon-Weaver, and Richness indices following the community level physiological profiling from Biolog EcoPlate™. The analyses were done on three occasions corresponding to the growth stages of: 5–6 leaf, flowering, and pod formation. The enzymatic activities were higher in I than NI (p < 0.05) throughout the growing season. However, none of the functional diversity indices differed significantly under both treatments, regardless of the growth stage. This work showed that the functional diversity of the microbial communities was a less sensitive tool than enzyme activities in assessment of rhizobial inoculation effects on rhizosphere microbial activity. PMID:27213363

  5. Evaluation of pulmonary nodules in Asian population

    PubMed Central

    Phua, Chee K.; Sim, Wen Y.; Sen Tee, Kuan; Lew, Sennen J. W.; Lim, Albert Y. H.; Tai, Dessmon Y. H.; Goh, Soon Keng; Kor, Ai Ching; Ng, Alan W. K.; Abisheganaden, John

    2016-01-01

    Background American College of Chest Physicians (ACCP) provides guidelines to manage pulmonary nodules. Pulmonary nodules however can be malignant or benign. Similar incidence of tuberculosis (TB) and lung cancer in Asian countries raises concern over the relevance of suggested guidelines in Asian population. There is little data on the pattern of clinical practice in the management of pulmonary nodules in Asian country (Singapore). Our study describes the current pattern of clinical practice in this area highlighting the variation in practice and discussing the potential reasons. Methods Retrospective review of the medical records of patients diagnosed with lung cancer in 2010. Results Sixty nodules were identified in 32 patients. Nodules were detected incidentally on routine imaging in 7 (21.9%) patients. TB contact tracing and pre-employment screening were common ways by which nodules were detected incidentally. Over one third (37.5%) were non-smokers. Majority of nodules were located in the upper lobes of right and left lung followed by right lower lobe (RLL). Only few patients 8 (25%) had positron emission tomography (PET) scan for staging purposes. There were no difference in survival between patients who presented with single, 747 (range, 25–1,840) days vs. multiple nodules 928 (range, 30–2,572) days, P=0.26. In a retrospective analysis of malignancy risk with the probability calculator, 62.5% patients were at low-moderate risk whilst 32.5% were at high risk. Conclusions The clinical practice of managing pulmonary nodules in Asian population differs from ACCP guidelines. None of the patient had pre-test probability calculated, and few had PET scan. This is because upper lobe predominance of lung cancer is identical to TB, non-smoking history does not have any weight in discounting malignancy risk where many of the Asian lung cancer patients are non-smokers, and the local endemicity of TB and its confounding effect on radiological findings of CT scan and

  6. CT features of pleural masses and nodules.

    PubMed

    Reetz, Jennifer A; Buza, Elizabeth L; Krick, Erika L

    2012-01-01

    Pleural space masses and nodules are rarely described on computed tomography (CT) in veterinary medicine and have only been described in patients with neoplasia. Our purpose was to describe the CT findings and diagnoses in seven patients with pleural masses and nodules. Two patients had broad-based, plaque-like pleural masses, both of which were due to neoplasia (primary pleural carcinoma, metastatic thymoma). Two patients had well-defined pleural nodules and nodular pleural thickening, one of which had mesothelial hypertrophy, and another of which had metastatic hemangiosarcoma. Three patients had ill-defined pleural nodules to nodular pleural thickening, one of which had metastatic pulmonary carcinoma, while the other two had bacterial infection with mesothelial proliferation (n = 2), fibrinous pleuritis (n = 1), and severe mediastinal pleuritis/mediastinitis (n = 2). Five of the seven patients had focal, multifocal or diffuse smooth, and/or irregular pleural thickening. Five of seven patients had pleural effusion, and postcontrast CT was useful in several patients for delineating the pleural lesions from the effusion. All patients except one had additional lesions identified on CT besides those in the pleural space. CT is useful in identifying and characterizing pleural space lesions and could be used to guide further diagnostic procedures such as thoracoscopy or exploratory thoracotomy. Both neoplastic and nonneoplastic diseases should be considered in the differential diagnoses for pleural space masses and nodules found on CT. PMID:22092656

  7. Effectiveness and limitations of core needle biopsy in the diagnosis of thyroid nodules: review of current literature.

    PubMed

    Yoon, Jung Hyun; Kim, Eun-Kyung; Kwak, Jin Young; Moon, Hee Jung

    2015-05-01

    Fine needle aspiration (FNA) is currently accepted as an easy, safe, and reliable tool for the diagnosis of thyroid nodules. Nonetheless, a proportion of FNA samples are categorized into non-diagnostic or indeterminate cytology, which frustrates both the clinician and patient. To overcome this limitation of FNA, core needle biopsy (CNB) of the thyroid has been proposed as an additional diagnostic method for more accurate and decisive diagnosis for thyroid nodules of concern. In this review, we focus on the effectiveness and limitations of CNB, and what factors should be considered when CNB is utilized in the diagnosis of thyroid nodules. PMID:26018514

  8. Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules.

    PubMed

    Rashid, M Harun-or; Young, J Peter W; Everall, Isobel; Clercx, Pia; Willems, Anne; Santhosh Braun, Markus; Wink, Michael

    2015-09-01

    Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnII) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA-DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA-DNA hybridization showed 50-62% relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoli) and 50-60% relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92% with their close relatives and 88-89% with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T) = LMG 28441(T) = DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T) = LMG 28442(T) = DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T) = LMG 28443(T) = DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae. PMID:26060217

  9. Pulmonary nodules and metastases in colorectal cancer.

    PubMed

    Nordholm-Carstensen, Andreas

    2016-01-01

    prevalence of and risk factors for SPCM in a Danish nationwide cohort of patients with newly diagnosed CRC from 2001 to 2011. SPCM were detected in 7.5% of the patients and in 37% of these cases the metastatic spread was confined to the lungs. The prevalence of SPCM increased with the implementation of thoracic CT in CRC staging. SPCM impaired survival significantly and was associated with increasing age and rectal cancer. Resection of the primary tumour, resection of the SPCM and treatment with chemotherapy were associated with improved survival. Unfortunately, however, only very few patients were subjected to all three treatment measures, and the improved prognosis could simply be the result of a selection bias. The inter-observer variation in classification of findings at thoracic CT scans was investigated in study III and was based on staging CT scans from a local cohort of patients with newly diagnosed CRC. Based on an experienced thoracic radiologist's assessment of the scans, we searched for radiological characteristics of IPN that could predict malignancy of the nodule. There was a significant difference in the number of IPNs detected between the primary and the thoracic radiologist's assessment. The thoracic radiologist classified fewer nodules as IPN and even reported with higher specificity and sensitivity for SPCM. More than 20% of IPNs (as classified by the thoracic radiologist) proved to be SPCM. Unfortunately, no radiological characteristics could be associated with a malignant outcome. In continuation of these findings we suggested a secondary review of scans with IPN be a group of dedicated thoracic radiologists. This approach might reduce the need for additional work-up for IPN and calls for clarification in future prospective studies. Identification of patients in particular risk of SPCM could be of value in the assessment of pulmonary nodules. Several biomarkers have been proposed for differential metastatic patterns in CRC. In study IV we investigated

  10. Role of electromagnetic navigational bronchoscopy in pulmonary nodule management.

    PubMed

    Goud, Aditya; Dahagam, Chanukya; Breen, David P; Sarkar, Saiyad

    2016-07-01

    The incidence of pulmonary nodules and lung cancer is rising. Some of this increase in incidence is due to improved pick up by newer imaging modalities. However, the goal is to diagnose these lesion, many of which are located in the periphery, by safe and relatively non-invasive methods. This has led to the emergence of numerous techniques such as electromagnetic navigational bronchoscopy (ENB). Current evidence supports a role for these techniques in the diagnostic pathway. However, numerous factor influence the diagnostic accuracy. Thus despite significant advances, more research needs to be undertaken to further improve the currently available diagnostic technologies. PMID:27606080