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Sample records for sinorhizobium meliloti nodulation

  1. Biogeography of Sinorhizobium meliloti nodulating alfalfa in different Croatian regions.

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    Donnarumma, Francesca; Bazzicalupo, Marco; Blažinkov, Mihaela; Mengoni, Alessio; Sikora, Sanjia; Babić, Katarina Huić

    2014-09-01

    Sinorhizobium meliloti is a nitrogen-fixing rhizobium symbiont of legumes, widespread in many temperate environments the high genetic diversity of which enables it to thrive as a symbiont of host legumes and free-living in soil. Soil type, together with geographic differences and host plant genotype, seem to be prominent factors in shaping rhizobial genetic diversity. While a large body of research supports the idea that the genetic structure of free-living microbial taxa exhibits a clear biogeographic pattern, few investigations have been performed on the biogeographic pattern of S. meliloti genotypes in a restricted geographic range. In the present study, a collection of 128 S. meliloti isolates from three different regions in Croatia was investigated to analyze the relationship between genetic diversity, geographic distribution, soil features and isolate phenotypes by using amplified fragment length polymorphism (AFLP) as a genome-wide scanning method. Results obtained led to the conclusion that the genotypes of isolates cluster according to the region of origin and that the differentiation of S. meliloti populations can be mainly ascribed to geographic isolation following an isolation-by-distance model, with a strong distance-decay relationship of genetic similarity with distance, in which local soil conditions are not the major component influencing the isolate phenotypes or their genomic differentiation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  2. Inability To Catabolize Galactose Leads to Increased Ability To Compete for Nodule Occupancy in Sinorhizobium meliloti

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    Geddes, Barney A.

    2012-01-01

    A mutant unable to utilize galactose was isolated in Sinorhizobium meliloti strain Rm1021. The mutation was found to be in a gene annotated dgoK1, a putative 2-keto-3-deoxygalactonokinase. The genetic region was isolated on a complementing cosmid and subsequently characterized. Based on genetic and bioinformatic evidence, the locus encodes all five enzymes (galD, dgoK, dgoA, SMc00883, and ilvD1) involved in the De Ley-Doudoroff pathway for galactose catabolism. Although all five genes are present, genetic analysis suggests that the galactonase (SMc00883) and the dehydratase (ilvD1) are dispensable with respect to the ability to catabolize galactose. In addition, we show that the transport of galactose is partially facilitated by the arabinose transporter (AraABC) and that both glucose and galactose compete with arabinose for transport. Quantitative reverse transcription-PCR (qRT-PCR) data show that in a dgoK background, the galactose locus is constitutively expressed, and the induction of the ara locus seems to be enhanced. Assays of competition for nodule occupancy show that the inability to catabolize galactose is correlated with an increased ability to compete for nodule occupancy. PMID:22797764

  3. [Factor analysis of interactions between alfalfa nodule bacteria (Sinorhizobium meliloti) genes that regulate symbiotic nitrogen fixation].

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    Provorov, N A; Chuklina, E; Vorob'ev, N I; Onishchuk, O P; Simarov, B V

    2013-04-01

    Factor analysis has been conducted for the data on the interaction between the genes of the root nodule bacteria (rhizobia), which influence the efficiency of symbiosis with leguminous plants, including dctA (encoding succinate permease), dctBD (activating the dctA gene due to binding its enhancer in the presence of succinate), rpoN (activating the promoters of dctA and nitrogenase genes nifHDK), and nifA (activating the nitrogenase genes due to binding their enhancers). The analysis of the alfalfa rhizobia (Sinorhizobium meliloti) recombinants that contain additional copies ofthese genes suggested the antagonistic (epistatic) interaction between nifA and rpoN. It may be associated either with the competition for C compounds imported into the nodules between the energy production and nitrogen assimilation processes or with the competition for redox potentials between the oxidative phosphorylation and nitrogen fixation processes. Since the phenotypic effects of the studied genes depend on the activity of nitrogen export into the aerial parts of plants, we suppose that its accumulation in bacteroids impairs the activation of the nifHDK genes by the NifA protein due to its interaction with the GlnB protein (the nitrogen metabolism regulator) or with the FixLJ and ActSR proteins (the redox potential regulators).

  4. Genotypic characterization of indigenous Sinorhizobium meliloti and ...

    African Journals Online (AJOL)

    The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of alfalfa (Medicago sativa L.) and sulla (Hedysarum sp.) forage legumes, respectively, were isolated from root nodules and soils from Morocco. We used three PCR-based techniques namely, rep-PCR, RAPD and ARDRA ...

  5. A Sinorhizobium meliloti-specific N-acyl homoserine lactone quorum-sensing signal increases nodule numbers in Medicago truncatula independent of autoregulation

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    Debora Fabiola Veliz Vallejos

    2014-10-01

    Full Text Available N-acyl homoserine lactones (AHLs act as quorum sensing signals that regulate cell-density dependent behaviors in many gram-negative bacteria, in particular those important for plant-microbe interactions. AHLs can also be recognized by plants, and this may influence their interactions with bacteria. Here we tested whether the exposure to AHLs affects the nodule-forming symbiosis between legume hosts and rhizobia. We treated roots of the model legume, Medicago truncatula, with a range of AHLs either from its specific symbiont, Sinorhizobium meliloti, or from the potential pathogens, Pseudomonas aeruginosa and Agrobacterium vitis. We found increased numbers of nodules formed on root systems treated with the S. meliloti-specific AHL, 3-oxo-C14-homoserine lactone, at a concentration of 1 μM, while the other AHLs did not result in significant changes to nodule numbers. We did not find any evidence for altered nodule invasion by the rhizobia. Quantification of flavonoids that could act as nod gene inducers in S. meliloti did not show any correlation with increased nodule numbers. The effects of AHLs were specific for an increase in nodule numbers, but not lateral root numbers or root length. Increased nodule numbers following 3-oxo-C14-homoserine lactone treatment were under control of autoregulation of nodulation and were still observed in the autoregulation mutant, sunn4 (super numeric nodules4. However, increases in nodule numbers by 3-oxo-C14-homoserine lactone were not found in the ethylene-insensitive sickle mutant. A comparison between M. truncatula with M. sativa (alfalfa and Trifolium repens (white clover showed that the observed effects of AHLs on nodule numbers were specific to M. truncatula, despite M. sativa nodulating with the same symbiont. We conclude that plant perception of the S. meliloti-specific 3-oxo-C14-homoserine lactone influences nodule numbers in M. truncatula via an ethylene-dependent, but autoregulation

  6. The tep1 gene of Sinorhizobium meliloti coding for a putative transmembrane efflux protein and N-acetyl glucosamine affect nod gene expression and nodulation of alfalfa plants

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    Soto María

    2009-01-01

    Full Text Available Abstract Background Soil bacteria collectively known as Rhizobium, characterized by their ability to establish beneficial symbiosis with legumes, share several common characteristics with pathogenic bacteria when infecting the host plant. Recently, it was demonstrated that a fadD mutant of Sinorhizobium meliloti is altered in the control of swarming, a type of co-ordinated movement previously associated with pathogenicity, and is also impaired in nodulation efficiency on alfalfa roots. In the phytopathogen Xanthomonas campestris, a fadD homolog (rpfB forms part of a cluster of genes involved in the regulation of pathogenicity factors. In this work, we have investigated the role in swarming and symbiosis of SMc02161, a S. meliloti fadD-linked gene. Results The SMc02161 locus in S. meliloti shows similarities with members of the Major Facilitator Superfamily (MFS of transporters. A S. meliloti null-mutant shows increased sensitivity to chloramphenicol. This indication led us to rename the locus tep1 for transmembrane efflux protein. The lack of tep1 does not affect the appearance of swarming motility. Interestingly, nodule formation efficiency on alfalfa plants is improved in the tep1 mutant during the first days of the interaction though nod gene expression is lower than in the wild type strain. Curiously, a nodC mutation or the addition of N-acetyl glucosamine to the wild type strain lead to similar reductions in nod gene expression as in the tep1 mutant. Moreover, aminosugar precursors of Nod factors inhibit nodulation. Conclusion tep1 putatively encodes a transmembrane protein which can confer chloramphenicol resistance in S. meliloti by expelling the antibiotic outside the bacteria. The improved nodulation of alfalfa but reduced nod gene expression observed in the tep1 mutant suggests that Tep1 transports compounds which influence nodulation. In contrast to Bradyrhizobium japonicum, we show that in S. meliloti there is no feedback regulation

  7. PCR Analysis of "expR" Gene Regulating Biosynthesis of Exopolysaccharides in "Sinorhizobium Meliloti"

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    Sorroche, Fernando G.; Giordano, Walter

    2012-01-01

    Exopolysaccharide (EPS) production by the rhizobacterium "Sinorhizobium meliloti" is essential for root nodule formation on its legume host (alfalfa), and for establishment of a nitrogen-fixing symbiosis between the two partners. Production of EPS II (galactoglucan) by certain "S. meliloti" strains results in a mucoid colony…

  8. A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

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    Queiroux Clothilde

    2012-05-01

    Full Text Available Abstract Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

  9. Sinorhizobium meliloti can protect Medicago truncatula against Phoma medicaginis attack

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    Moncef MRABET

    2011-09-01

    Full Text Available The Sinorhizobium meliloti microsymbiont of Medicago spp. was used in an antibiosis test against Phoma medicaginis and in bioprotection assays of Medicago truncatula JA17 from the pathogen. Among 17 S. meliloti strains isolated from root nodules of M. truncatula and Medicago laciniata grown in Tunisian soils, six showed up to 60% growth inhibition of five P. medicaginis strains isolated from infected field-grown M. truncatula. Two S. meliloti strains with differing in vitro effects on P. medicaginis, 10.16/R6 antagonist and 5M6 non antagonist, were used in a bioprotection assay of M. truncatula JA17 from the pathogen. The inoculation of P. medicaginis caused complete root and stem rotting, and the mortality of all treated plantlets. Inoculation of the antagonist S. meliloti strain 10.16/R6 to M. truncatula JA17 infected with P. medicaginis was associated with a significant 65% decrease of vegetative rotting length, an 80% decrease of plant mortality, an increase of root length, and enhancement of root and shoot biomass comparatively to control plantlets treated with P. medicaginis. The inoculation of the non antagonistic S. meliloti strain 5M6 slightly decreased disease and slightly increased plant growth parameters.

  10. Genetic Identification and Symbiotic Efficiency of an Indigenous Sinorhizobium meliloti Field Population

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    Sanja Sikora

    2003-01-01

    Full Text Available Soil bacteria Sinorhizobium meliloti are of enormous agricultural value, because of their ability to fix atmospheric nitrogen in symbiosis with an important forage crop legume – alfalfa. The main aim of this study was (i to isolate indigenous S. meliloti strains from different field sites in Croatia, (ii to assess genetic diversity and genetic relationships amongst strains of natural populations and (iii to provide information about nodulation and symbiotic efficiency of indigenous S. meliloti strains. The nine strains isolated from alfalfa nodules collected from different field sites and three reference strains were analysed. Genetic characterisation by PCR-RFLP of the 16S rDNA, rep-PCR and RAPD-PCR was applied to study the status of Sinorhizobium meliloti populations inhabiting nodules of alfalfa. The results of PCR-RFLP of the 16S rDNA revealed that all isolates belong to the S. meliloti species. Cluster analysis of rep-PCR and RAPD-PCR profiles showed significant differences among S. meliloti isolates. Both methods resulted in identical grouping of strains. Among indigenous strains two divergent groups could be determined. The biggest differences were detected among two reference strains and all field isolates. Greenhouse studies were performed for evaluation of symbiotic efficiency and compatibility of S. meliloti strains with two alfalfa cultivars. Quantitative expression of symbiotic efficiency was evaluated by measurement of nodule dry weight, content of proteins and total nitrogen in plants, dry matter and green mass yield of plants. All strains nodulated both alfalfa cultivars but with different efficiency. Significant differences in dry matter and green mass yield of alfalfa as well as protein content were determined depending on the strain used. The results indicate that three indigenous S. meliloti strains can be characterised as the most efficient of all strains used in this study.

  11. Symbiotic Nitrogen Fixation in Alfalfa (Medicago Sativa L.) by Sinorhizobium Meliloti at Al-Qassim Regions, Saudi Arabia

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    Al-Barakah, F. N.; Mridha, M. A. U.

    2016-01-01

    The nodulation status in alfalfa (Medicago sativa L.) plants by Sinorhizobium meliloti under Saudi field condition was assessed in some selected farms in four seasons for two years. In the present study, we also monitored the introduced S. meliloti strains activity under Saudi soil conditions. The samples were collected at regular seasonal intervals from the selected farms. The total number of nodules, morphology of the nodules and the effectiveness of N/sub 2/-fixation was assessed. In general, it was revealed that soils in the selected areas in Saudi Arabia have sufficient bacteria of the proper types to nodulate the alfalfa plants. These nodules are high in number, small in size and white in color. The nodules obtained from most of the selected farms are ineffective for nitrogen fixation. Inoculation of alfalfa seeds with imported S. meliloti strains failed to fix the atmospheric nitrogen sufficiently and also the growth improvement of alfalfa plants. There was a wide variation in the occurrence of number of nodules among the four seasons in two years. It was also observed that summer season severely affected the nodulation making it nearly zero. This low number of nodules exerts a very slow recovery of nodule formation in the next year. The introduced strains were always over competing with the native strains but they did not survive because of hot and dry summer. Nitrogenase activity of the nodules collected from both the inoculated and non-inoculated farms were always very low in all the collected samples, which indicates that the ability of fixing nitrogen by S. meliloti strains in alfalfa under Saudi soils conditions is very low. (author)

  12. The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa

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    Jiménez-Zurdo José I

    2010-03-01

    Full Text Available Abstract Background The bacterial Hfq protein is able to interact with diverse RNA molecules, including regulatory small non-coding RNAs (sRNAs, and thus it is recognized as a global post-transcriptional regulator of gene expression. Loss of Hfq has an extensive impact in bacterial physiology which in several animal pathogens influences virulence. Sinorhizobium meliloti is a model soil bacterium known for its ability to establish a beneficial nitrogen-fixing intracellular symbiosis with alfalfa. Despite the predicted general involvement of Hfq in the establishment of successful bacteria-eukaryote interactions, its function in S. meliloti has remained unexplored. Results Two independent S. meliloti mutants, 2011-3.4 and 1021Δhfq, were obtained by disruption and deletion of the hfq gene in the wild-type strains 2011 and 1021, respectively, both exhibiting similar growth defects as free-living bacteria. Transcriptomic profiling of 1021Δhfq revealed a general down-regulation of genes of sugar transporters and some enzymes of the central carbon metabolism, whereas transcripts specifying the uptake and metabolism of nitrogen sources (mainly amino acids were more abundant than in the wild-type strain. Proteomic analysis of the 2011-3.4 mutant independently confirmed these observations. Symbiotic tests showed that lack of Hfq led to a delayed nodulation, severely compromised bacterial competitiveness on alfalfa roots and impaired normal plant growth. Furthermore, a large proportion of nodules (55%-64% elicited by the 1021Δhfq mutant were non-fixing, with scarce content in bacteroids and signs of premature senescence of endosymbiotic bacteria. RT-PCR experiments on RNA from bacteria grown under aerobic and microoxic conditions revealed that Hfq contributes to regulation of nifA and fixK1/K2, the genes controlling nitrogen fixation, although the Hfq-mediated regulation of fixK is only aerobiosis dependent. Finally, we found that some of the recently

  13. Interaction between Nitrogen and Phosphate Stress Responses in Sinorhizobium meliloti

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    Kelly Lynn Hagberg

    2016-11-01

    Full Text Available Bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. While both the Nitrogen Stress Response (NSR and Phosphate Stress Response (PSR have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in Sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. The PII proteins, GlnB and GlnK, regulate the NSR activity, but analysis of global transcription changes in a PII deficient mutant suggest that the S. meliloti PII proteins may also regulate the PSR. PII double deletion mutants grow very slowly and pseudoreversion of the slow growth phenotype is common. To understand this phenomenon better, transposon mutants were isolated that had a faster growing phenotype. One mutation was in phoB, the response regulator for a two component regulatory system that is important in the PSR. phoB::Tn5 mutants had different phenotypes in the wild type compared to a PII deficient background. This led to the hypothesis that phosphate stress affects the NSR and conversely, that nitrogen stress affects the PSR. Our results show that phosphate availability affects glutamine synthetase activity and expression, which are often used as indicators of NSR activity, but that nitrogen availability did not affect alkaline phosphatase activity and expression, which are indicators of PSR activity. We conclude that the NSR is co-regulated by nitrogen and phosphate, whereas the PSR does not appear to be co-regulated by nitrogen in addition to its known phosphate regulation.

  14. [Occurrence of islands in genomes of Sinorhizobium meliloti native isolates].

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    Muntyan, V S; Cherkasova, M E; Andronov, E E; Simarov, B V; Roumiantseva, M L

    2016-10-01

    Genomes of 184 Sinorhizobium meliloti native isolates were studied to test the occurence of islands Sme21T, Sme19T, and Sme80S previously described in the model strain Rm1021. This analysis was conducted using PCR methodology involving specific primers. It was demonstrated that, in the examined geographically distinct populations of S. meliloti from the Northern Caucasus (NCG) and the Aral Sea region (PAG), the strains containing genomic islands were observed with similar frequency (0.55 and 0.57, respectively). Island Sme80S, denoted as an island of “environmental adaptivity,” was identified predominantly (frequency of 0.38) in genomes of strains which exhibited a lower level of salt tolerance and was isolated in PAG, a modern center of introgressive hybridization of alfalfa subjected to salinity. Island Sme21T designated as “ancestral” was observed in genomes of strains isolated in NCG, the primary center of host-plant biodiversity, 10-fold more often than in strains from PAG. An island Sme19T, which predominantly carries genes encoding transposases, was observed in genomes of strains in both populations with average frequency of 0.10. The analysis of linkage disequilibrium (LD) based on the assessment of probability for detection of different islands combinations in genomes revealed an independent inheritance of islands in salt-sensitive strains of various geographic origin. In contrast, the absence of this trend was noted in the majority of the examined combinations of salt-tolerant strains. It was concluded that the structure of chromosome in PAG strains which predominantly possessed a salt-sensitive phenotype was subjected to active recombinant processes, which could predetermine the intensity of microevolutionary processes in bacterial populations and facilitate an adaptation of bacteria in adverse environmental effect.

  15. Role of quorum sensing in Sinorhizobium meliloti-Alfalfa symbiosis.

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    Gurich, Nataliya; González, Juan E

    2009-07-01

    The ExpR/Sin quorum-sensing system of the gram-negative soil bacterium Sinorhizobium meliloti plays an important role in the establishment of symbiosis with its host plant Medicago sativa. A mutant unable to produce autoinducer signal molecules (sinI) is deficient in its ability to invade the host, but paradoxically, a strain lacking the quorum-sensing transcriptional regulator ExpR is as efficient as the wild type. We compared the whole-genome expression profile of the wild-type strain with strains missing one of the quorum-sensing regulatory components to identify genes controlled by the ExpR/Sin system throughout the different phases of the bacterial growth cycle, as well as in planta. Our analyses revealed that ExpR is a highly versatile regulator with a unique ability to show different regulatory capabilities in the presence or absence of an autoinducer. In addition, this study provided us with insight into the plant invasion defect displayed by the autoinducer mutant. We also discovered that the ExpR/Sin quorum-sensing system is repressed after plant invasion. Therefore, quorum sensing plays a crucial role in the regulation of many cell functions that ensures the successful invasion of the host and is inactivated once symbiosis is established.

  16. Altered susceptibility to infection by Sinorhizobium meliloti and Nectria haematococca in alfalfa roots with altered cell cycle.

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    Woo, H-H; Hirsch, A M; Hawes, M C

    2004-07-01

    Most infections of plant roots are initiated in the region of elongation; the mechanism for this tissue-specific localization pattern is unknown. In alfalfa expressing PsUGT1 antisense mRNA under the control of the cauliflower mosaic virus (CaMV) 35S promoter, the cell cycle in roots is completed in 48 h instead of 24 h, and border cell number is decreased by more than 99%. These plants were found to exhibit increased root-tip infection by a fungal pathogen and reduced nodule formation by a bacterial symbiont. Thus, the frequency of infection in the region of elongation by Nectria haematocca was unaffected, but infection of the root tip was increased by more than 90%; early stages of Sinorhizobium meliloti infection and nodule morphology were normal, but the frequency of nodulation was fourfold lower than in wild-type roots.

  17. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

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    Galardini, Marco [University of Florence; Mengoni, Alessio [University of Florence; Brilli, Matteo [Universite de Lyon, France; Pini, Francesco [University of Florence; Fioravanti, Antonella [University of Florence; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Teshima, Hazuki [Los Alamos National Laboratory (LANL); Mocali, Stefano [Agrobiol & Pedol Ctr ABP, Agr Res Council, I-50121 Florence, Italy; Bazzicalupo, Marco [University of Florence; Biondi, Emanuele [University of Florence

    2011-01-01

    Background: Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. Results: With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.

  18. Malic enzyme cofactor and domain requirements for symbiotic N2 fixation by Sinorhizobium meliloti.

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    Mitsch, Michael J; Cowie, Alison; Finan, Turlough M

    2007-01-01

    The NAD(+)-dependent malic enzyme (DME) and the NADP(+)-dependent malic enzyme (TME) of Sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid N-terminal region homologous to other malic enzymes and a 330-amino-acid C-terminal region with similarity to phosphotransacetylase enzymes (PTA). We have shown previously that dme mutants of S. meliloti fail to fix N(2) (Fix(-)) in alfalfa root nodules, whereas tme mutants are unimpaired in their N(2)-fixing ability (Fix(+)). Here we report that the amount of DME protein in bacteroids is 10 times greater than that of TME. We therefore investigated whether increased TME activity in nodules would allow TME to function in place of DME. The tme gene was placed under the control of the dme promoter, and despite elevated levels of TME within bacteroids, no symbiotic nitrogen fixation occurred in dme mutant strains. Conversely, expression of dme from the tme promoter resulted in a large reduction in DME activity and symbiotic N(2) fixation. Hence, TME cannot replace the symbiotic requirement for DME. In further experiments we investigated the DME PTA-like domain and showed that it is not required for N(2) fixation. Thus, expression of a DME C-terminal deletion derivative or the Escherichia coli NAD(+)-dependent malic enzyme (sfcA), both of which lack the PTA-like region, restored wild-type N(2) fixation to a dme mutant. Our results have defined the symbiotic requirements for malic enzyme and raise the possibility that a constant high ratio of NADPH + H(+) to NADP in nitrogen-fixing bacteroids prevents TME from functioning in N(2)-fixing bacteroids.

  19. Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco

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    Udupa Sripada M

    2010-01-01

    Full Text Available Abstract Background Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.. In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco. Results RsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM, water stress (-1.5 MPa, high temperature (40°C and low pH (3.5, respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline. The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P Conclusion High degree of phenotypic and genotypic diversity is present in S

  20. Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides

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    Markus F. F. Arnold

    2017-08-01

    Full Text Available The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis. However, the mechanisms used by S. meliloti to resist antimicrobial activity of plant peptides are poorly understood. To address this, we applied a global genetic approach using transposon mutagenesis followed by high-throughput sequencing (Tn-seq to identify S. meliloti genes and pathways that increase or decrease bacterial competitiveness during exposure to the well-studied cationic NCR247 peptide and also to the unrelated model antimicrobial peptide polymyxin B. We identified 78 genes and several diverse pathways whose interruption alters S. meliloti resistance to NCR247. These genes encode the following: (i cell envelope polysaccharide biosynthesis and modification proteins, (ii inner and outer membrane proteins, (iii peptidoglycan (PG effector proteins, and (iv non-membrane-associated factors such as transcriptional regulators and ribosome-associated factors. We describe a previously uncharacterized yet highly conserved peptidase, which protects S. meliloti from NCR247 and increases competitiveness during symbiosis. Additionally, we highlight a considerable number of uncharacterized genes that provide the basis for future studies to investigate the molecular basis of symbiotic development as well as chronic pathogenic interactions.

  1. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

    Directory of Open Access Journals (Sweden)

    Daligault Hajnalka

    2011-05-01

    Full Text Available Abstract Background Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. Results With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB, AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. Conclusions In conclusions, the extended comparative genomics approach revealed a

  2. Sinorhizobium meliloti putA Gene Regulation: a New Model within the Family Rhizobiaceae

    OpenAIRE

    Soto, María José; Jiménez-Zurdo, José Ignacio; van Dillewijn, Pieter; Toro, Nicolás

    2000-01-01

    Proline dehydrogenase (PutA) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. In Sinorhizobium meliloti, as in other microorganisms, the putA gene is transcriptionally activated in response to proline. In Rhodobacter capsulatus, Agrobacterium, and most probably in Bradyrhizobium, this activation is dependent on an Lrp-like protein encoded by the putR gene, located immediately upstream of putA. Interestingly, sequence and genetic analysis of the region upstream of...

  3. The effect of phosphate deficiency on quorum sensing signaling pathway of Sinorhizobium meliloti

    OpenAIRE

    Najmeh Pakdaman; akbar mostajeran

    2015-01-01

      Introduction : Phosphorus is one of the most essential macroelements for bacterial cells. Since phosphate (PO4-3) limitation is frequently encountered in soils, bacteria developed some mechanisms in response to this sever condition. Phosphate transporter (PstS) and proteins involved in quorum sensing (QS) signaling pathway are affected by mediating PhoB, response regulator, following phosphate starvation. QS system of Sinorhizobium meliloti composed of at least three genes of sinI (autoindu...

  4. Three way interactions between Thymus vulgaris, Medicago truncatula and Sinorhizobium meliloti

    OpenAIRE

    Grøndahl, Eva; Ehlers, Bodil Kirstine

    2012-01-01

    Thymus vulgaris is a dominating component of the Mediterranean garrigue vegetation. It produces aromatic oil, containing monoterpenes, which affects the performance (growth, survival) of other plants, and microorganisms. Annual plant species of the genus Medicago are commonly found in Mediterranean thyme communities; in fact they often grow very close to thyme plants (within 1 square meter). Medicago has a symbiosis with the nitrogen fixing bacteria Sinorhizobium meliloti – which is essential...

  5. Biodegradable plastics from Sinorhizobium meliloti as plastics compatible with the environment and human health

    Directory of Open Access Journals (Sweden)

    Mehrdad Hashemi Beidokhti

    2016-03-01

    Full Text Available Introduction: Polyhydroxyalkanoates (PHAs are natural polyesters and biodegradable plastics that are stored as intracellular inclusion bodies by a great variety of bacteria. The aim of this study was to extract polyhydroxyalkanoate from native Sinorhizobium meliloti in Iran. Materials and methods: Sinorhizobium meliloti isolates were collected from roots of alfalfa plants and were identified by Gram staining, biochemical experiments and amplification of 1500 bp fragment of 16Sr DNA gene. PHA granules were detected by microscopic examination. PHA production was evaluated in nutrient deficient medium and its amount was determined by conversion of PHA into crotonic acid by sulphuric acid treatment. The effect of various temperatures, agitation rate and carbon source (sucrose, mannitol, and maltose were evaluated on dry cell weight and polyhydroxybutyrate (PHB production. Results: The maximum amount of polymer production (43.10% was seen in basal mineral medium at 29°C, pH~7 and 215 revolutions per minute (rpm. The results of this research showed that the S5 isolate was capable to produce maximum poly3- hydroxybutyrate. The produced polymer was analyzed for its purity by GC- mass (gas chromatography- mass spectroscopy and confirmed to be PHB compared with the standard polymer. Discussion and conclusion: Native strains of Sinorhizobium can be used in the production of biodegradable plastics and the results of present study showed that S. meliloti S5 was capable to produce maximum PHB at 29°C, agitation rate of 215 rpm, and pH~7. 

  6. MALDI mass spectrometry-assisted molecular imaging of metabolites during nitrogen fixation in the Medicago truncatula-Sinorhizobium meliloti symbiosis.

    Science.gov (United States)

    Ye, Hui; Gemperline, Erin; Venkateshwaran, Muthusubramanian; Chen, Ruibing; Delaux, Pierre-Marc; Howes-Podoll, Maegen; Ané, Jean-Michel; Li, Lingjun

    2013-07-01

    Symbiotic associations between leguminous plants and nitrogen-fixing rhizobia culminate in the formation of specialized organs called root nodules, in which the rhizobia fix atmospheric nitrogen and transfer it to the plant. Efficient biological nitrogen fixation depends on metabolites produced by and exchanged between both partners. The Medicago truncatula-Sinorhizobium meliloti association is an excellent model for dissecting this nitrogen-fixing symbiosis because of the availability of genetic information for both symbiotic partners. Here, we employed a powerful imaging technique - matrix-assisted laser desorption/ionization (MALDI)/mass spectrometric imaging (MSI) - to study metabolite distribution in roots and root nodules of M. truncatula during nitrogen fixation. The combination of an efficient, novel MALDI matrix [1,8-bis(dimethyl-amino) naphthalene, DMAN] with a conventional matrix 2,5-dihydroxybenzoic acid (DHB) allowed detection of a large array of organic acids, amino acids, sugars, lipids, flavonoids and their conjugates with improved coverage. Ion density maps of representative metabolites are presented and correlated with the nitrogen fixation process. We demonstrate differences in metabolite distribution between roots and nodules, and also between fixing and non-fixing nodules produced by plant and bacterial mutants. Our study highlights the benefits of using MSI for detecting differences in metabolite distributions in plant biology. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  7. In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction.

    Science.gov (United States)

    Zhao, Hansheng; Li, Mao; Fang, Kechi; Chen, Wenfeng; Wang, Jing

    2012-01-01

    Sinorhizobium meliloti is a soil bacterium, known for its capability to establish symbiotic nitrogen fixation (SNF) with leguminous plants such as alfalfa. S. meliloti 1021 is the most extensively studied strain to understand the mechanism of SNF and further to study the legume-microbe interaction. In order to provide insight into the metabolic characteristics underlying the SNF mechanism of S. meliloti 1021, there is an increasing demand to reconstruct a metabolic network for the stage of SNF in S. meliloti 1021. Through an iterative reconstruction process, a metabolic network during the stage of SNF in S. meliloti 1021 was presented, named as iHZ565, which accounts for 565 genes, 503 internal reactions, and 522 metabolites. Subjected to a novelly defined objective function, the in silico predicted flux distribution was highly consistent with the in vivo evidences reported previously, which proves the robustness of the model. Based on the model, refinement of genome annotation of S. meliloti 1021 was performed and 15 genes were re-annotated properly. There were 19.8% (112) of the 565 metabolic genes included in iHZ565 predicted to be essential for efficient SNF in bacteroids under the in silico microaerobic and nutrient sharing condition. As the first metabolic network during the stage of SNF in S. meliloti 1021, the manually curated model iHZ565 provides an overview of the major metabolic properties of the SNF bioprocess in S. meliloti 1021. The predicted SNF-required essential genes will facilitate understanding of the key functions in SNF and help identify key genes and design experiments for further validation. The model iHZ565 can be used as a knowledge-based framework for better understanding the symbiotic relationship between rhizobia and legumes, ultimately, uncovering the mechanism of nitrogen fixation in bacteroids and providing new strategies to efficiently improve biological nitrogen fixation.

  8. Sinorhizobium meliloti putA gene regulation: a new model within the family Rhizobiaceae.

    Science.gov (United States)

    Soto, M J; Jiménez-Zurdo, J I; van Dillewijn, P; Toro, N

    2000-04-01

    Proline dehydrogenase (PutA) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. In Sinorhizobium meliloti, as in other microorganisms, the putA gene is transcriptionally activated in response to proline. In Rhodobacter capsulatus, Agrobacterium, and most probably in Bradyrhizobium, this activation is dependent on an Lrp-like protein encoded by the putR gene, located immediately upstream of putA. Interestingly, sequence and genetic analysis of the region upstream of the S. meliloti putA gene did not reveal such a putR locus or any other encoded transcriptional activator of putA. Furthermore, results obtained with an S. meliloti putA null mutation indicate the absence of any proline-responsive transcriptional activator and that PutA serves as an autogenous repressor. Therefore, the model of S. meliloti putA regulation completely diverges from that of its Rhizobiaceae relatives and resembles more that of enteric bacteria. However, some differences have been found with the latter model: (i) S. meliloti putA gene is not catabolite repressed, and (ii) the gene encoding for the major proline permease (putP) does not form part of an operon with the putA gene.

  9. Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry.

    Science.gov (United States)

    Barsch, Aiko; Patschkowski, Thomas; Niehaus, Karsten

    2004-10-01

    A metabolite analysis of the soil bacterium Sinorhizobium meliloti was established as a first step towards a better understanding of the symbiosis with its host plant Medicago truncatula. A crucial step was the development of fast harvesting and extraction methods for the bacterial metabolites because of rapid changes in their composition. S. meliloti 1021 cell cultures grown in minimal medium were harvested by centrifugation, filtration or immediate freezing in liquid nitrogen followed by a lyophilisation step. Bacteria were lysed mechanically in methanol and hydrophilic compounds were analysed after methoxymation and silylisation via GC-MS. The different compounds were identified by comparison with the NIST 98 database and available standards. From about 200 peaks in each chromatogram 65 compounds have been identified so far. A comparison of the different extraction methods giving the metabolite composition revealed clear changes in several amino acids and amino acid precursor pools. A principal component analysis (PCA) was able to distinguish S. meliloti cells grown on different carbon sources based on their metabolite profile. A comparison of the metabolite composition of a S. meliloti leucine auxotrophic mutant with the wild type revealed a marked accumulation of 2-isopropylmalate in the mutant. Interestingly, the accumulated metabolite is not the direct substrate of the mutated enzyme, 3-isopropylmalate dehydrogenase, but the substrate of isopropylmalate isomerase, which acts one step further upstream in the biosynthetic pathway of leucine. This finding further emphasises the importance of integrating metabolic data into post-genomic research.

  10. Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by theTrans-Encoded Small RNA MmgR.

    Science.gov (United States)

    Lagares, Antonio; Ceizel Borella, Germán; Linne, Uwe; Becker, Anke; Valverde, Claudio

    2017-04-15

    Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans -encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti , over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for M akes m ore g ranules R egulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR ( mmgR Δ33-51 ). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans -encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti

  11. Cloning-free genome engineering in Sinorhizobium meliloti advances applications of Cre/loxP site-specific recombination.

    Science.gov (United States)

    Döhlemann, Johannes; Brennecke, Meike; Becker, Anke

    2016-09-10

    The soil-dwelling α-proteobacterium Sinorhizobium meliloti serves as model for studies of symbiotic nitrogen fixation, a highly important process in sustainable agriculture. Here, we report advancements of the genetic toolbox accelerating genome editing in S. meliloti. The hsdMSR operon encodes a type-I restriction-modification (R-M) system. Transformation of S. meliloti is counteracted by the restriction endonuclease HsdR degrading DNA which lacks the appropriate methylation pattern. We provide a stable S. meliloti hsdR deletion mutant showing enhanced transformation with Escherichia coli-derived plasmid DNA and demonstrate that using an E. coli plasmid donor, expressing S. meliloti methyl transferase genes, is an alternative strategy of increasing the transformation efficiency of S. meliloti. Furthermore, we devise a novel cloning-free genome editing (CFGE) method for S. meliloti, Agrobacterium tumefaciens and Xanthomonas campestris, and demonstrate the applicability of this method for intricate applications of the Cre/lox recombination system in S. meliloti. An enhanced Cre/lox system, allowing for serial deletions of large genomic regions, was established. An assay of lox spacer mutants identified a set of lox sites mediating specific recombination. The availability of several non-promiscuous Cre recognition sites enables simultaneous specific Cre/lox recombination events. CFGE combined with Cre/lox recombination is put forward as powerful approach for targeted genome editing, involving serial steps of manipulation to expedite the genetic accessibility of S. meliloti as chassis. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Quantitative Proteomic Analysis of the Hfq-Regulon in Sinorhizobium meliloti 2011

    Science.gov (United States)

    Sobrero, Patricio; Schlüter, Jan-Philip; Lanner, Ulrike; Schlosser, Andreas; Becker, Anke; Valverde, Claudio

    2012-01-01

    Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the α-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with 15N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti. PMID:23119037

  13. Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase.

    Directory of Open Access Journals (Sweden)

    Tao Liu

    Full Text Available Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 63:28:5, in 77 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation in proteins involved in processes related to rhizobial adaptation was also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis, ActR (pH stress and microaerobic adaption, SupA (potassium stress, chaperonin GroEL2 (viability and potentially symbiosis, and ExoP (succinoglycan synthesis and secretion. These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.

  14. Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa.

    Science.gov (United States)

    van Dillewijn, Pieter; Villadas, Pablo J; Toro, Nicolás

    2002-09-01

    The success of a rhizobial inoculant in the soil depends to a large extent on its capacity to compete against indigenous strains. M403, a Sinorhizobium meliloti strain with enhanced competitiveness for nodule occupancy, was recently constructed by introducing a plasmid containing an extra copy of a modified putA (proline dehydrogenase) gene. This strain and M401, a control strain carrying the same plasmid without the modified gene, were used as soil inoculants for alfalfa in a contained field release experiment at León, Spain. In this study, we determined the effects of these two strains on the indigenous microbial community. 16S rRNA genes were obtained from the rhizosphere of alfalfa inoculated with strain M403 or strain M401 or from noninoculated plants by amplification of DNA from soil with bacterial group-specific primers. These genes were analyzed and compared by restriction fragment length polymorphism and temperature gradient gel electrophoresis. The results allowed us to differentiate between alterations in the microbial community apparently caused by inoculation and by the rhizosphere effect and seasonal fluctuations induced by the alfalfa plants and by the environment. Only moderate inoculation-dependent effects could be detected, while the alfalfa plants appeared to have a much stronger influence on the microbial community.

  15. Three way interactions between Thymus vulgaris, Medicago truncatula and Sinorhizobium meliloti

    DEFF Research Database (Denmark)

    Grøndahl, Eva; Ehlers, Bodil Kirstine

    2012-01-01

    thyme communities; in fact they often grow very close to thyme plants (within 1 square meter). Medicago has a symbiosis with the nitrogen fixing bacteria Sinorhizobium meliloti – which is essential for nitrogen uptake in the nutrient poor garrigue. The aim of this study was to examine 1) if Medicago...... experienced ones, irrespective of whether the soil was amended with thyme oil or not. Furthermore, there was a small, but significant difference in Medicago fitness between naive and experienced plant genotypes on soil amended with thyme oil. Thyme experienced Medicago genotypes performed better on thyme soil......Thymus vulgaris is a dominating component of the Mediterranean garrigue vegetation. It produces aromatic oil, containing monoterpenes, which affects the performance (growth, survival) of other plants, and microorganisms. Annual plant species of the genus Medicago are commonly found in Mediterranean...

  16. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains

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    Landry Christian R

    2005-11-01

    Full Text Available Abstract Background Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa. This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusion The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.

  17. The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

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    Rodriguez-Llorente Ignacio

    2009-06-01

    Full Text Available Abstract Background Rhizobium-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered. Results Here we present an analysis of the 'Symbiosis Interactome' using novel computational methods in order to address the complex dynamic interactions between proteins involved in the symbiosis of the model bacteria Sinorhizobium meliloti with its plant hosts. Our study constitutes the first large-scale analysis attempting to reconstruct this complex biological process, and to identify novel proteins involved in establishing symbiosis. We identified 263 novel proteins potentially associated with the Symbiosis Interactome. The topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The contribution of a set of novel proteins was tested analyzing the symbiotic properties of several S. meliloti mutants. We found mutants with altered symbiotic phenotypes suggesting novel proteins that provide key complementary roles for symbiosis. Conclusion Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases.

  18. Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114

    International Nuclear Information System (INIS)

    Martínez-Rodríguez, Sergio; González-Ramírez, Luis Antonio; Clemente-Jiménez, Josefa María; Rodríguez-Vico, Felipe; Las Heras-Vázquez, Francisco Javier; Gavira, Jose A.; García-Ruíz, Juan Manuel

    2006-01-01

    The dihydropyrimidinase from S. meliloti CECT4114, with activity towards both hydantoin and dihydrouracil substrates, was crystallized, and diffraction data were collected to 1.85 Å resolution. Dihydropyrimidinases are involved in the reductive pathway of pyrimidine degradation, catalysing the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamoyl β-amino acids. This enzyme has often been referred to as hydantoinase owing to its industrial application in the production of optically pure amino acids starting from racemic mixtures of 5-monosubstituted hydantoins. Recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been expressed, purified and crystallized. Crystallization was performed using the counter-diffusion method with capillaries of 0.3 mm inner diameter. Crystals of SmelDhp suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to ensure mass transport controlled by diffusion. X-ray data were collected to a resolution of 1.85 Å. The crystal belongs to the orthorhombic space group C222 1 , with unit-cell parameters a = 124.89, b = 126.28, c = 196.10 Å and two molecules in the asymmetric unit. A molecular-replacement solution has been determined and refinement is in progress

  19. Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Rodríguez, Sergio [Departamento de Química Física, Bioquímica y Química Inorgánica, Área de Bioquímica y Biología Molecular, Edificio CITE I, Universidad de Almería (Spain); González-Ramírez, Luis Antonio [Laboratorio de Estudios Cristalográficos-IACT, CSIC-UGRA, P. T. Ciencias de la Salud, Granada 18100 (Spain); Clemente-Jiménez, Josefa María; Rodríguez-Vico, Felipe; Las Heras-Vázquez, Francisco Javier [Departamento de Química Física, Bioquímica y Química Inorgánica, Área de Bioquímica y Biología Molecular, Edificio CITE I, Universidad de Almería (Spain); Gavira, Jose A.; García-Ruíz, Juan Manuel, E-mail: jmgruiz@ugr.es [Laboratorio de Estudios Cristalográficos-IACT, CSIC-UGRA, P. T. Ciencias de la Salud, Granada 18100 (Spain); Departamento de Química Física, Bioquímica y Química Inorgánica, Área de Bioquímica y Biología Molecular, Edificio CITE I, Universidad de Almería (Spain)

    2006-12-01

    The dihydropyrimidinase from S. meliloti CECT4114, with activity towards both hydantoin and dihydrouracil substrates, was crystallized, and diffraction data were collected to 1.85 Å resolution. Dihydropyrimidinases are involved in the reductive pathway of pyrimidine degradation, catalysing the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamoyl β-amino acids. This enzyme has often been referred to as hydantoinase owing to its industrial application in the production of optically pure amino acids starting from racemic mixtures of 5-monosubstituted hydantoins. Recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been expressed, purified and crystallized. Crystallization was performed using the counter-diffusion method with capillaries of 0.3 mm inner diameter. Crystals of SmelDhp suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to ensure mass transport controlled by diffusion. X-ray data were collected to a resolution of 1.85 Å. The crystal belongs to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 124.89, b = 126.28, c = 196.10 Å and two molecules in the asymmetric unit. A molecular-replacement solution has been determined and refinement is in progress.

  20. Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti

    Directory of Open Access Journals (Sweden)

    Chiara Santi

    2017-12-01

    Full Text Available Plant lipid-transfer proteins (LTPs are small basic secreted proteins, which are characterized by lipid-binding capacity and are putatively involved in lipid trafficking. LTPs play a role in several biological processes, including the root nodule symbiosis. In this regard, the Medicago truncatula nodulin 5 (MtN5 LTP has been proved to positively regulate the nodulation capacity, controlling rhizobial infection and nodule primordia invasion. To better define the lipid transfer protein MtN5 function during the symbiosis, we produced MtN5-downregulated and -overexpressing plants, and we analysed the transcriptomic changes occurring in the roots at an early stage of Sinorhizobium meliloti infection. We also carried out the lipid profile analysis of wild type (WT and MtN5-overexpressing roots after rhizobia infection. The downregulation of MtN5 increased the root hair curling, an early event of rhizobia infection, and concomitantly induced changes in the expression of defence-related genes. On the other hand, MtN5 overexpression favoured the invasion of the nodules by rhizobia and determined in the roots the modulation of genes that are involved in lipid transport and metabolism as well as an increased content of lipids, especially galactolipids that characterize the symbiosome membranes. Our findings suggest the potential participation of LTPs in the synthesis and rearrangement of membranes occurring during the formation of the infection threads and the symbiosome membrane.

  1. Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti.

    Science.gov (United States)

    Santi, Chiara; Molesini, Barbara; Guzzo, Flavia; Pii, Youry; Vitulo, Nicola; Pandolfini, Tiziana

    2017-12-19

    Plant lipid-transfer proteins (LTPs) are small basic secreted proteins, which are characterized by lipid-binding capacity and are putatively involved in lipid trafficking. LTPs play a role in several biological processes, including the root nodule symbiosis. In this regard, the Medicago truncatula nodulin 5 (MtN5) LTP has been proved to positively regulate the nodulation capacity, controlling rhizobial infection and nodule primordia invasion. To better define the lipid transfer protein MtN5 function during the symbiosis, we produced MtN5-downregulated and -overexpressing plants, and we analysed the transcriptomic changes occurring in the roots at an early stage of Sinorhizobium meliloti infection. We also carried out the lipid profile analysis of wild type (WT) and MtN5-overexpressing roots after rhizobia infection. The downregulation of MtN5 increased the root hair curling, an early event of rhizobia infection, and concomitantly induced changes in the expression of defence-related genes. On the other hand, MtN5 overexpression favoured the invasion of the nodules by rhizobia and determined in the roots the modulation of genes that are involved in lipid transport and metabolism as well as an increased content of lipids, especially galactolipids that characterize the symbiosome membranes. Our findings suggest the potential participation of LTPs in the synthesis and rearrangement of membranes occurring during the formation of the infection threads and the symbiosome membrane.

  2. 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interaction.

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    L David Kuykendall

    Full Text Available Sinorhizobium meliloti strain 1021, a nitrogen-fixing, root-nodulating bacterial microsymbiont of alfalfa, has a 3.5 Mbp circular chromosome and two megaplasmids including 1.3 Mbp pSymA carrying nonessential 'accessory' genes for nitrogen fixation (nif, nodulation and host specificity (nod. A related bacterium, psyllid-vectored 'Ca. Liberibacter asiaticus,' is an obligate phytopathogen with a reduced genome that was previously analyzed for genes orthologous to genes on the S. meliloti circular chromosome. In general, proteins encoded by pSymA genes are more similar in sequence alignment to those encoded by S. meliloti chromosomal orthologs than to orthologous proteins encoded by genes carried on the 'Ca. Liberibacter asiaticus' genome. Only two 'Ca. Liberibacter asiaticus' proteins were identified as having orthologous proteins encoded on pSymA but not also encoded on the chromosome of S. meliloti. These two orthologous gene pairs encode a Na(+/K+ antiporter (shared with intracellular pathogens of the family Bartonellacea and a Co++, Zn++ and Cd++ cation efflux protein that is shared with the phytopathogen Agrobacterium. Another shared protein, a redox-regulated K+ efflux pump may regulate cytoplasmic pH and homeostasis. The pSymA and 'Ca. Liberibacter asiaticus' orthologs of the latter protein are more highly similar in amino acid alignment compared with the alignment of the pSymA-encoded protein with its S. meliloti chromosomal homolog. About 182 pSymA encoded proteins have sequence similarity (≤ E-10 with 'Ca. Liberibacter asiaticus' proteins, often present as multiple orthologs of single 'Ca. Liberibacter asiaticus' proteins. These proteins are involved with amino acid uptake, cell surface structure, chaperonins, electron transport, export of bioactive molecules, cellular homeostasis, regulation of gene expression, signal transduction and synthesis of amino acids and metabolic cofactors. The presence of multiple orthologs defies mutational

  3. Interaction between Nitrogen and Phosphate Stress Responses inSinorhizobium meliloti.

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    Hagberg, Kelly L; Yurgel, Svetlana N; Mulder, Monika; Kahn, Michael L

    2016-01-01

    Bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. While both the nitrogen stress response (NSR) and phosphate stress response (PSR) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in Sinorhizobium meliloti , a facultatively symbiotic, nitrogen-fixing bacteria. The P II proteins, GlnB and GlnK, regulate the NSR activity, but analysis of global transcription changes in a P II deficient mutant suggest that the S. meliloti P II proteins may also regulate the PSR. P II double deletion mutants grow very slowly and pseudoreversion of the slow growth phenotype is common. To understand this phenomenon better, transposon mutants were isolated that had a faster growing phenotype. One mutation was in phoB , the response regulator for a two component regulatory system that is important in the PSR. phoB ::Tn 5 mutants had different phenotypes in the wild type compared to a P II deficient background. This led to the hypothesis that phosphate stress affects the NSR and conversely, that nitrogen stress affects the PSR. Our results show that phosphate availability affects glutamine synthetase activity and expression, which are often used as indicators of NSR activity, but that nitrogen availability did not affect alkaline phosphatase activity and expression, which are indicators of PSR activity. We conclude that the NSR is co-regulated by nitrogen and phosphate, whereas the PSR does not appear to be co-regulated by nitrogen in addition to its known phosphate regulation.

  4. Alfalfa forage digestibility, quality and yield under future climate change scenarios vary with Sinorhizobium meliloti strain.

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    Sanz-Sáez, Álvaro; Erice, Gorka; Aguirreolea, Jone; Muñoz, Fernando; Sánchez-Díaz, Manuel; Irigoyen, Juan José

    2012-05-15

    Elevated CO(2) may decrease alfalfa forage quality and in vitro digestibility through a drop in crude protein and an enhancement of fibre content. The aim of the present study was to analyse the effect of elevated CO(2), elevated temperature and Sinorhizobium meliloti strains (102F78, 102F34 and 1032 GMI) on alfalfa yield, forage quality and in vitro dry matter digestibility. This objective is in line with the selection of S. meliloti strains in order to maintain high forage yield and quality under future climate conditions. Plants inoculated with the 102F34 strain showed more DM production than those inoculated with 1032GMI; however, these strains did not show significant differences with 102F78 plants. Neutral or acid detergent fibres were not enhanced in plants inoculated with the 102F34 strain under elevated CO(2) or temperature and hence, in vitro dry matter digestibility was unaffected. Crude protein content, an indicator of forage quality, was negatively related to shoot yield. Plants inoculated with 102F78 showed a similar shoot yield to those inoculated with 102F34, but had higher crude protein content at elevated CO(2) and temperature. Under these climate change conditions, 102F78 inoculated plants produced higher quality forage. However, the higher digestibility of plants inoculated with the 102F34 strain under any CO(2) or temperature conditions makes them more suitable for growing under climate change conditions. In general, elevated CO(2) in combination with high temperature (Climate Change scenario) reduced IVDMD and CP content and enhanced fibre content, which means that animal production will be negatively affected. Copyright © 2012 Elsevier GmbH. All rights reserved.

  5. The effect of phosphate deficiency on quorum sensing signaling pathway of Sinorhizobium meliloti

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    Najmeh Pakdaman

    2015-02-01

    Full Text Available   Introduction : Phosphorus is one of the most essential macroelements for bacterial cells. Since phosphate (PO4-3 limitation is frequently encountered in soils, bacteria developed some mechanisms in response to this sever condition. Phosphate transporter (PstS and proteins involved in quorum sensing (QS signaling pathway are affected by mediating PhoB, response regulator, following phosphate starvation. QS system of Sinorhizobium meliloti composed of at least three genes of sinI (autoinducer synthase, sinR and expR (autoinducer activated receptor which involved in its free living and symbiotic functions .   Materials and method s: The optical density (OD600 of different S. meliloti transformed strains carrying pLK004 (a pstS promoter-egfp fusion, pLK64 (a sinI promoter-egfp fusion, pLK65 (a sinR promoter-egfp fusion, pLK66 (an expR promoter-egfp fusion and control (promoterless-egfp fusion plasmids were read under different phosphate concentrations of 0.1 (phosphate deficiency, 0.5 and 2 mM (sufficient phosphate at several time points of 16, 24 and 40h. The promoter activity of different genes of pstS, sinI, sinR and expR were measured as emitted fluorescence per bacterial cell density (OD600 under different phosphate concentrations .   Results : By reducing phosphate concentration in the medium, the growth rate of transformed bacteria decreased, especially at 40h. The promoter activity of pstS, sinI and sinR, but not expR, genes was activated following phosphate starvation .   Discussion and conclusion : S. meliloti can upregulate PstS to partly compensate phosphate deficiency in the environment. The gene of sinR is also activated in a PhoB dependent manner as phosphate starvation is encountered. SinR is the activator of sinI, so the upregulation of QS pathway under phosphate deficiency may be facilitate free living and symbiotic bacterial functions .

  6. Role of extracellular compounds in Cd-sequestration relative to Cd uptake by bacterium Sinorhizobium meliloti

    Energy Technology Data Exchange (ETDEWEB)

    Slaveykova, Vera I., E-mail: vera.slaveykova@epfl.c [Environmental Biophysical Chemistry, IIE-ENAC, Ecole Polytechnique Federale de Lausanne (EPFL), Station 2, CH-1015 Lausanne (Switzerland); Parthasarathy, Nalini [Department of Inorganic, Analytic and Applied Chemistry, University of Geneva, Sciences II, 30 Quai Ernest Ansermet, 1211 Geneva 4 (Switzerland); Dedieu, Karine; Toescher, Denis [Environmental Biophysical Chemistry, IIE-ENAC, Ecole Polytechnique Federale de Lausanne (EPFL), Station 2, CH-1015 Lausanne (Switzerland)

    2010-08-15

    The role of bacterially derived compounds in Cd(II) complexation and uptake by bacterium Sinorhizobium meliloti wild type (WT) and genetically modified ExoY-mutant, deficient in exopolysaccharide production, was explored combining chemical speciation measurements and assays with living bacteria. Obtained results demonstrated that WT- and ExoY-strains excreted siderophores in comparable amounts, while WT-strain produced much higher amount of exopolysaccharides and less exoproteins. An evaluation of Cd(II) distribution in bacterial suspensions under short term exposure conditions, showed that most of the Cd is bound to bacterial surface envelope, including Cd bound to the cell wall and to the attached extracellular polymeric substances. However, the amount of Cd bound to the dissolved extracellular compounds increases at high Cd(II) concentrations. The implications of these findings to more general understanding of the Cd(II) fate and cycling in the environment is discussed. - Bacterial excreted extracellular compounds play minor role in Cd(II) sequestration relative to bacteria.

  7. [The effect of combined and separate inoculation of alfalfa plants with Azospirillum lipoferum and Sinorhizobium meliloti on denitrification and nitrogen-fixing activities].

    Science.gov (United States)

    Furina, E K; Bonartseva, G A

    2007-01-01

    The effects of associative nitrogen fixer Azospirillum lipoferum strain 137 and root nodule bacteria Sinorhizobium meliloti after combined and separate inoculation of alfalfa seedlings on the background of mineral nitrogen applied at various times were studied. It was demonstrated that exudates of the alfalfa seedlings with the first pair of cotyledonary leaves already provide a high activity of these bacteria in the rhizosphere. To 74.6% of the introduced nitrate was transformed into N2O when the binary preparation of these bacteria was used. In an extended experiment (30 days), an active reduction of nitrates to N2O (11 micromol N2O/pot x 24 h) with inhibition of nitrogen fixation was observed in all of the experimental variants during the formation of legume-rhizobial and associative symbioses and simultaneous introduction of nitrates and bacteria. The most active enzyme fixation was observed in the case of a late (after 14 days) application of nitrates in the variants with both separate inoculations and inoculation with the binary preparation of A. lipoferum and S. meliloti. Separation in time of the application of bacterial preparations and mineral nitrogen assisted its preservation in all of the experimental variants. The variant of alfalfa inoculation with the binary preparation of A. lipoferum and S. meliloti and application of nitrates 2 weeks after inoculation was optimal for active nitrogen fixation (224.7 C2H4 nmol/flask x 24 h) and low denitrification activity (1.8 x micromol N2O/flask x 24 h). These results are useful in applied developments aimed at the use of bacterial and mineral fertilizers for leguminous plants.

  8. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation

    OpenAIRE

    Saramago, Margarida; Peregrina, Alexandra; Robledo, Marta; Matos, Rute G.; Hilker, Rolf; Serrania, Javier; Becker, Anke; Arraiano, Cecilia M.; Jim?nez-Zurdo, Jos? I.

    2016-01-01

    Abstract Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously...

  9. Identification and characterization of the intracellular poly-3-hydroxybutyrate depolymerase enzyme PhaZ of Sinorhizobium meliloti

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    Zachertowska Alicja

    2010-03-01

    Full Text Available Abstract Background S. meliloti forms indeterminate nodules on the roots of its host plant alfalfa (Medicago sativa. Bacteroids of indeterminate nodules are terminally differentiated and, unlike their non-terminally differentiated counterparts in determinate nodules, do not accumulate large quantities of Poly-3-hydroxybutyrate (PHB during symbiosis. PhaZ is in intracellular PHB depolymerase; it represents the first enzyme in the degradative arm of the PHB cycle in S. meliloti and is the only enzyme in this half of the PHB cycle that remains uncharacterized. Results The S. meliloti phaZ gene was identified by in silico analysis, the ORF was cloned, and a S. meliloti phaZ mutant was constructed. This mutant exhibited increased PHB accumulation during free-living growth, even when grown under non-PHB-inducing conditions. The phaZ mutant demonstrated no reduction in symbiotic capacity; interestingly, analysis of the bacteroids showed that this mutant also accumulated PHB during symbiosis. This mutant also exhibited a decreased capacity to tolerate long-term carbon starvation, comparable to that of other PHB cycle mutants. In contrast to other PHB cycle mutants, the S. meliloti phaZ mutant did not exhibit any decrease in rhizosphere competitiveness; however, this mutant did exhibit a significant increase in succinoglycan biosynthesis. Conclusions S. meliloti bacteroids retain the capacity to synthesize PHB during symbiosis; interestingly, accumulation does not occur at the expense of symbiotic performance. phaZ mutants are not compromised in their capacity to compete for nodulation in the rhizosphere, perhaps due to increased succinoglycan production resulting from upregulation of the succinoglycan biosynthetic pathway. The reduced survival capacity of free-living cells unable to access their accumulated stores of PHB suggests that PHB is a crucial metabolite under adverse conditions.

  10. An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti.

    Science.gov (United States)

    Cowie, Alison; Cheng, Jiujun; Sibley, Christopher D; Fong, Ying; Zaheer, Rahat; Patten, Cheryl L; Morton, Richard M; Golding, G Brian; Finan, Turlough M

    2006-11-01

    As a means of investigating gene function, we developed a robust transcription fusion reporter vector to measure gene expression in bacteria. The vector, pTH1522, was used to construct a random insert library for the Sinorhizobium meliloti genome. pTH1522 replicates in Escherichia coli and can be transferred to, but cannot replicate in, S. meliloti. Homologous recombination of the DNA fragments cloned in pTH1522 into the S. meliloti genome generates transcriptional fusions to either the reporter genes gfp(+) and lacZ or gusA and rfp, depending on the orientation of the cloned fragment. Over 12,000 fusion junctions in 6,298 clones were identified by DNA sequence analysis, and the plasmid clones were recombined into S. meliloti. Reporter enzyme activities following growth of these recombinants in complex medium (LBmc) and in minimal medium with glucose or succinate as the sole carbon source allowed the identification of genes highly expressed under one or more growth condition and those expressed at very low to background levels. In addition to generating reporter gene fusions, the vector allows Flp recombinase-directed deletion formation and gene disruption, depending on the nature of the cloned fragment. We report the identification of genes essential for growth on complex medium as deduced from an inability to recover recombinants from pTH1522 clones that carried fragments internal to gene or operon transcripts. A database containing all the gene expression activities together with a web interface showing the precise locations of reporter fusion junctions has been constructed (www.sinorhizobium.org).

  11. Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Babić, Katarina Huić; Schauss, Kristina; Hai, Brigitte; Sikora, Sanja; Redzepović, Sulejman; Radl, Viviane; Schloter, Michael

    2008-11-01

    Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.

  12. Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols.

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    Alexandre Bourdès

    Full Text Available Förster resonance energy transfer (FRET biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens. To expand the number of available FRET biosensors we used the induction profile of the Sinorhizobium meliloti transportome to systematically screen for new FRET biosensors.Two new vectors were developed for cloning genes for solute-binding proteins (SBPs between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2 and red fluorescent protein (mKate2 FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, myo-inositol, L-rhamnose, L-fucose, β-diglucosides (cellobiose and gentiobiose, D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate. To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP transport systems.FRET based on orange (mOrange2 and red fluorescent protein (mKate2 partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i cyclic polyols, (ii L-deoxy sugars, (iii β-linked disaccharides and (iv C4-dicarboxylates could be developed to study metabolism in vivo.

  13. Competitive Advantage Provided by Bacterial Motility in the Formation of Nodules by Rhizobium meliloti

    Science.gov (United States)

    Ames, Peter; Bergman, Kostia

    1981-01-01

    The effect of motility on the competitive success of Rhizobium meliloti in nodule production was investigated. A motile strain formed more nodules than expected when mixed at various unfavorable ratios with either flagellated or nonflagellated nonmotile derivatives. We conclude that motility confers a selective advantage on rhizobia when competing with nonmotile strains. PMID:7298580

  14. Transcriptome Response to Heavy Metals in Sinorhizobium meliloti CCNWSX0020 Reveals New Metal Resistance Determinants That Also Promote Bioremediation by Medicago lupulina in Metal-Contaminated Soil.

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    Lu, Mingmei; Jiao, Shuo; Gao, Enting; Song, Xiuyong; Li, Zhefei; Hao, Xiuli; Rensing, Christopher; Wei, Gehong

    2017-10-15

    The symbiosis of the highly metal-resistant Sinorhizobium meliloti CCNWSX0020 and Medicago lupulina has been considered an efficient tool for bioremediation of heavy metal-polluted soils. However, the metal resistance mechanisms of S. meliloti CCNWSX00200 have not been elucidated in detail. Here we employed a comparative transcriptome approach to analyze the defense mechanisms of S. meliloti CCNWSX00200 against Cu or Zn exposure. Six highly upregulated transcripts involved in Cu and Zn resistance were identified through deletion mutagenesis, including genes encoding a multicopper oxidase (CueO), an outer membrane protein (Omp), sulfite oxidoreductases (YedYZ), and three hypothetical proteins (a CusA-like protein, a FixH-like protein, and an unknown protein), and the corresponding mutant strains showed various degrees of sensitivity to multiple metals. The Cu-sensitive mutant (Δ cueO ) and three mutants that were both Cu and Zn sensitive (Δ yedYZ , Δ cusA -like, and Δ fixH -like) were selected for further study of the effects of these metal resistance determinants on bioremediation. The results showed that inoculation with the Δ cueO mutant severely inhibited infection establishment and nodulation of M. lupulina under Cu stress, while inoculation with the Δ yedYZ and Δ fixH -like mutants decreased just the early infection frequency and nodulation under Cu and Zn stresses. In contrast, inoculation with the Δ cusA -like mutant almost led to loss of the symbiotic capacity of M. lupulina to even grow in uncontaminated soil. Moreover, the antioxidant enzyme activity and metal accumulation in roots of M. lupulina inoculated with all mutants were lower than those with the wild-type strain. These results suggest that heavy metal resistance determinants may promote bioremediation by directly or indirectly influencing formation of the rhizobium-legume symbiosis. IMPORTANCE Rhizobium-legume symbiosis has been promoted as an appropriate tool for bioremediation of heavy

  15. Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvI and its phenotypic characteristics.

    Science.gov (United States)

    Wang, Chunxia; Kemp, Jocelyn; Da Fonseca, Isabel O; Equi, Raymie C; Sheng, Xiaoyan; Charles, Trevor C; Sobral, Bruno W S

    2010-02-01

    Bacterial two-component regulatory systems (TCS) are common components of complex regulatory networks and cascades. In Sinorhizobium meliloti, the TCS ExoS/ChvI controls exopolysaccharide succinoglycan production and flagellum biosynthesis. Although this system plays a crucial role in establishing the symbiosis between S. meliloti and its host plant, it is not well characterized. Attempts to generate complete loss-of-function mutations in either exoS or chvI in S. meliloti have been unsuccessful; thus, it was previously suggested that exoS or chvI are essential genes for bacterial cell growth. We constructed a chvI mutant by completely deleting the open reading frame encoding this gene. The mutant strain failed to grow on complex medium, exhibited lower tolerance to acidic condition, produced significantly less poly-3-hydroxybutyrate than the wild type, was hypermotile, and exhibited an altered lipopolysaccharide profile. In addition, this mutant was defective in symbiosis with Medicago truncatula and M. sativa (alfalfa), although it induced root hair deformation as efficiently as the wild type. Together, our results demonstrate that ChvI is intimately involved in regulatory networks involving the cell envelope and metabolism; however, its precise role within the regulatory network remains to be determined.

  16. Contribution of NFP LysM domains to the recognition of Nod factors during the Medicago truncatula/Sinorhizobium meliloti symbiosis.

    Science.gov (United States)

    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.

  17. Contribution of NFP LysM domains to the recognition of Nod factors during the Medicago truncatula/Sinorhizobium meliloti symbiosis.

    Directory of Open Access Journals (Sweden)

    Sandra Bensmihen

    Full Text Available 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.

  18. Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021

    Science.gov (United States)

    2013-01-01

    Background Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters. Results Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti σ factors σ70, σ54, σH1, σH2, σE1, σE2, and σE9). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response σ factor, RpoE2 (σE2), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5′ RACE mapping. Conclusions By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, σ factors and other transcription factors, and regulatory RNAs. PMID:23497287

  19. Cultural conditions required for the induction of an adaptive acid-tolerance response (ATR) in Sinorhizobium meliloti and the question as to whether or not the ATR helps rhizobia improve their symbiosis with alfalfa at low pH.

    Science.gov (United States)

    Draghi, Walter O; Del Papa, María Florencia; Pistorio, Mariano; Lozano, Mauricio; de Los Angeles Giusti, María; Torres Tejerizo, Gonzalo A; Jofré, Edgardo; Boiardi, José Luis; Lagares, Antonio

    2010-01-01

    Sinorhizobium meliloti associates with Medicago and Melilotus species to develop nitrogen-fixing symbioses. The agricultural relevance of these associations, the worldwide distribution of acid soils, and the remarkable acid sensitivity of the microsymbiont have all stimulated research on the responses of the symbionts to acid environments. We show here that an adaptive acid-tolerance response (ATR) can be induced in S. meliloti, as shown previously for Sinorhizobium medicae, when the bacteria are grown in batch cultures at the slightly acid pH of 6.1. In marked contrast, no increased tolerance to hydrogen ions is obtained if rhizobia are grown in a chemostat under continuous cultivation at the same pH. The adaptive ATR appears as a complex process triggered by an increased hydrogen-ion concentration, but operative only if other--as yet unknown--concomitant factors that depend on the culture conditions are present (although not provided under continuous cultivation). Although the stability of the ATR and its influence on acid tolerance has been characterized in rhizobia, no data have been available on the effect of the adapted state on symbiosis. Coinoculation experiments showed that acid-adapted indicator rhizobia (ATR+) were present in >90% of the nodules when nodulation was performed at pH 5.6, representing a >30% increase in occupancy compared with a control test. We show that the ATR represents a clear advantage in competing for nodulation at low pH. It is not yet clear whether such an effect results from an improved performance in the acid environment during preinfection, an enhanced ability to initiate infections, or both conditions. The practical use of ATR+ rhizobia will depend on validation experiments with soil microcosms and on field testing, as well as on the possibility of preserving the physiology of ATR+ bacteria in inoculant formulations.

  20. pSymA-Dependent Mobilization of the Sinorhizobium meliloti pSymB Megaplasmid ▿ †

    Science.gov (United States)

    Blanca-Ordóñez, Helena; Oliva-García, Juan J.; Pérez-Mendoza, Daniel; Soto, María J.; Olivares, José; Sanjuán, Juan; Nogales, Joaquina

    2010-01-01

    Sinorhizobium meliloti 1021 carries two megaplasmids, pSymA of 1,354 kb and pSymB of 1,683 kb, which are essential in establishing symbiosis with its legume hosts and important for bacterial fitness in the rhizosphere. We have previously shown that pSymA is self-transmissible and that its conjugal functions are regulated by the transcriptional repressor RctA. Here, we show conjugal transfer of pSymB as an in trans mobilization event that requires the type IV secretion system encoded by pSymA. pSymB carries a functional oriT and an adjacent relaxase gene, traA2, that is also transcriptionally repressed by rctA. Both symbiotic megaplasmids would require the relaxase genes in cis with their respective oriTs to achieve the highest transfer efficiencies. PMID:20889746

  1. Crystallization and preliminary crystallographic studies of an active-site mutant hydantoin racemase from Sinorhizobium meliloti CECT4114

    International Nuclear Information System (INIS)

    Martínez-Rodríguez, Sergio; González-Ramírez, Luis Antonio; Clemente-Jiménez, Josefa María; Rodríguez-Vico, Felipe; Las Heras-Vázquez, Francisco Javier; Gavira, Jose Antonio; García-Ruiz, Juan Ma.

    2007-01-01

    Crystals of an active-site mutated hydantoin racemase from S. meliloti have been obtained in the presence and absence of d,l-5-isopropyl-hydantoin and characterized by X-ray diffraction. A recombinant active-site mutant of hydantoin racemase (C76A) from Sinorhizobium meliloti CECT 4114 (SmeHyuA) has been crystallized in the presence and absence of the substrate d,l-5-isopropyl hydantoin. Crystals of the SmeHyuA mutant suitable for data collection and structure determination were grown using the counter-diffusion method. X-ray data were collected to resolutions of 2.17 and 1.85 Å for the free and bound enzymes, respectively. Both crystals belong to space group R3 and contain two molecules of SmeHyuA per asymmetric unit. The crystals of the free and complexed SmeHyuA have unit-cell parameters a = b = 85.43, c = 152.37 Å and a = b = 85.69, c = 154.38 Å, crystal volumes per protein weight (V M ) of 1.94 and 1.98 Å 3 Da −1 and solvent contents of 36.7 and 37.9%, respectively

  2. Crystallization and preliminary crystallographic studies of an active-site mutant hydantoin racemase from Sinorhizobium meliloti CECT4114

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Rodríguez, Sergio [Department of Cellular and Molecular Interactions, Vrije Universiteit Brussel, 1050 Brussels (Belgium); Ultrastructure Laboratory, Vrije Universiteit Brussel, 1050 Brussels (Belgium); González-Ramírez, Luis Antonio [Laboratorio de Estudios Cristalográficos, IACT (CSIC-U. Granada), P. T. Ciencias de la Salud, Granada 18100 (Spain); Clemente-Jiménez, Josefa María; Rodríguez-Vico, Felipe; Las Heras-Vázquez, Francisco Javier [Departamento de Química Física, Bioquímica y Química Inorgánica, Área de Bioquímica y Biología Molecular, Edf. CITE I, Universidad de Almería (Spain); Gavira, Jose Antonio, E-mail: jgavira@ugr.es; García-Ruiz, Juan Ma. [Laboratorio de Estudios Cristalográficos, IACT (CSIC-U. Granada), P. T. Ciencias de la Salud, Granada 18100 (Spain); Department of Cellular and Molecular Interactions, Vrije Universiteit Brussel, 1050 Brussels (Belgium)

    2008-01-01

    Crystals of an active-site mutated hydantoin racemase from S. meliloti have been obtained in the presence and absence of d,l-5-isopropyl-hydantoin and characterized by X-ray diffraction. A recombinant active-site mutant of hydantoin racemase (C76A) from Sinorhizobium meliloti CECT 4114 (SmeHyuA) has been crystallized in the presence and absence of the substrate d,l-5-isopropyl hydantoin. Crystals of the SmeHyuA mutant suitable for data collection and structure determination were grown using the counter-diffusion method. X-ray data were collected to resolutions of 2.17 and 1.85 Å for the free and bound enzymes, respectively. Both crystals belong to space group R3 and contain two molecules of SmeHyuA per asymmetric unit. The crystals of the free and complexed SmeHyuA have unit-cell parameters a = b = 85.43, c = 152.37 Å and a = b = 85.69, c = 154.38 Å, crystal volumes per protein weight (V{sub M}) of 1.94 and 1.98 Å{sup 3} Da{sup −1} and solvent contents of 36.7 and 37.9%, respectively.

  3. Phylogenetic distribution and evolutionary pattern of an α-proteobacterial small RNA gene that controls polyhydroxybutyrate accumulation in Sinorhizobium meliloti.

    Science.gov (United States)

    Lagares, Antonio; Roux, Indra; Valverde, Claudio

    2016-06-01

    It has become clear that sRNAs play relevant regulatory functions in bacteria. However, a comprehensive understanding of their biological roles considering evolutionary aspects has not been achieved for most of them. Thus, we have characterized the evolutionary and phylogenetic aspects of the Sinorhizobium meliloti mmgR gene encoding the small RNA MmgR, which has been recently reported to be involved in the regulation of polyhydroxybutyrate accumulation in this bacterium. We constructed a covariance model from a multiple sequence and structure alignment of mmgR close homologs that allowed us to extend the search and to detect further remote homologs of the sRNA gene. From our results, mmgR seemed to evolve from a common ancestor of the α-proteobacteria that diverged from the order of Rickettsiales. We have found mmgR homologs in most current species of α-proteobacteria, with a few exceptions in which genomic reduction events or gene rearrangements seem to explain its absence. Furthermore, a strong microsyntenic relationship was found between a large set of mmgR homologs and homologs of a gene encoding a putative N-formyl glutamate amidohydrolase (NFGAH) that allowed us to trace back the evolutionary path of this group of mmgR orthologs. Among them, structure and sequence traits have been completely conserved throughout evolution, namely a Rho-independent terminator and a 10-mer (5'-UUUCCUCCCU-3') that is predicted to remain in a single-stranded region of the sRNA. We thus propose the definition of the new family of α-proteobacterial sRNAs αr8, as well as the subfamily αr8s1 which encompass S. meliloti mmgR orthologs physically linked with the downstream open reading frame encoding a putative NFGAH. So far, mmgR is the trans-encoded small RNA with the widest phylogenetic distribution of well recognized orthologs among α-proteobacteria. Expression of the expected MmgR transcript in rhizobiales other than S. meliloti (Sinorhizobium fredii, Rhizobium

  4. Role of specific quorum-sensing signals in the regulation of exopolysaccharide II production within Sinorhizobium meliloti spreading colonies.

    Directory of Open Access Journals (Sweden)

    Mengsheng Gao

    Full Text Available BACKGROUND: Quorum sensing (QS in Sinorhizobium meliloti involves at least half a dozen different N-acyl homoserine lactone (AHL signals. These signals are produced by SinI, the sole AHL synthase in S. meliloti Rm8530. The sinI gene is regulated by two LuxR-type transcriptional regulators, SinR and ExpR. Mutations in sinI, sinR and expR abolish the production of exopolysaccharide II (EPS II. METHODOLOGY/PRINCIPAL FINDINGS: This study investigated a new type of coordinated surface spreading of Rm8530 that can be categorized as swarming. Motility assays on semi-solid surfaces revealed that both flagella and EPS II are required for this type of motility. The production of EPS II depends on AHLs produced by SinI. Of these AHLs, only C(16:1- and 3-oxo-C(16:1-homoserine lactones (HSLs stimulated swarming in an ExpR-dependent manner. These two AHLs induced the strongest response in the wggR reporter fusions. WggR is a positive regulator of the EPS II biosynthesis gene expression. The levels of the wggR activation correlated with the extent of swarming. Furthermore, swarming of S. meliloti required the presence of the high molecular weight (HMW fraction of EPS II. Within swarming colonies, a recombinase-based RIVET reporter in the wggR gene was resolved in 30% of the cells, indicating an enhanced regulation of EPS II production in the subpopulation of cells, which was sufficient to support swarming of the entire colony. CONCLUSIONS/SIGNIFICANCE: Swarming behavior of S. meliloti Rm8530 on semi-solid surfaces is found to be dependent on the functional QS regulatory cascades. Even though multiple AHL signals are produced by the bacterium, only two AHLs species, C(16:1- and 3-oxo-C(16:1-HSLs, affected swarming by up-regulating the expression of wggR. While EPS II is produced by Rm8530 as high and low molecular weight fractions, only the HMW EPS II facilitated initial stages of swarming, thus, suggesting a function for this polymer.

  5. Analysis of nodule meristem persistence and ENOD40 functioning in Medicago truncatula nodule formation

    NARCIS (Netherlands)

    Wan Xi,

    2007-01-01

    Medicago root nodules are formed as a result of the interaction of the plant with the soil-borne bacterium Sinorhizobium meliloti. Several plant genes are induced during nodule formation and MtENOD40 is one of the earliest genes activated. The precise function as well as the molecule

  6. Analysis of nodule meristem persistence and ENOD40 functioning in Medicago truncatula nodule formation

    NARCIS (Netherlands)

    Wan Xi,

    2007-01-01

    Medicago root nodules are formed as a result of the interaction of the plant with the soil-borne bacterium Sinorhizobium meliloti. Several plant genes are induced during nodule formation and MtENOD40 is one of the earliest genes activated. The precise function as well as the molecule harboring the

  7. Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti.

    Science.gov (United States)

    Zhang, Ye; Smallbone, Laura Anne; diCenzo, George C; Morton, Richard; Finan, Turlough M

    2016-07-26

    Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. Despite the wide distribution of these enzymes, their biological roles are unclear in part because the reaction catalyzed by these enzymes can be by-passed by other pathways. The N2-fixing alfalfa symbiont Sinorhizobium meliloti contains both a NAD(P)-malic enzyme (DME) and a separate NADP-malic enzyme (TME) and to help understand the role of these enzymes, we investigated growth, metabolomic, and transcriptional consequences resulting from loss of these enzymes in free-living cells. Loss of DME, TME, or both enzymes had no effect on growth with the glycolytic substrate, glucose. In contrast, the dme mutants, but not tme, grew slowly on the gluconeogenic substrate succinate and this slow growth was further reduced upon the addition of glucose. The dme mutant strains incubated with succinate accumulated trehalose and hexose sugar phosphates, secreted malate, and relative to wild-type, these cells had moderately increased transcription of genes involved in gluconeogenesis and pathways that divert metabolites away from the TCA cycle. While tme mutant cells grew at the same rate as wild-type on succinate, they accumulated the compatible solute putrescine. NAD(P)-malic enzyme (DME) of S. meliloti is required for efficient metabolism of succinate via the TCA cycle. In dme mutants utilizing succinate, malate accumulates and is excreted and these cells appear to increase metabolite flow via gluconeogenesis with a resulting increase in the levels of hexose-6-phosphates and trehalose. For cells utilizing succinate, TME activity alone appeared to be insufficient to produce the levels of pyruvate required for efficient TCA cycle metabolism. Putrescine was found to accumulate in tme cells growing with succinate, and whether this is related to altered levels of NADPH requires

  8. Effect of exogenous application of rhizopine on lucerne root nodulation

    African Journals Online (AJOL)

    Rhizopine, 3-0 -methyl scyllo-inosamine was applied to the roots of luceme seedling inoculated with either rhizopine synthesizing Sinorhizobium meliloti strain L530 or the non-rhizopine synthesizing strain Rm 1021 . There was an initial delay in nodule formation. A significant increase in the number of nodules formed in ...

  9. Symbiotic Properties of Sinorhizobium Fredii, J-TGS50 an Indonesian Soybean Nodule Forming Bacteria

    International Nuclear Information System (INIS)

    Setiyo Hadi Waluyo

    2004-01-01

    Green House experiments were conducted to study symbiotic properties of Sinorhizobium Fredii, J-TGS50. Sinorhizobium Fredii USDA 192, USDA 201, USDA 205, USDA 206, USDA 217 and Bradyrhizobium japonicum USDA 110 were used as references. Yeast extract mannitol broth culture of the bacteria were made and used as inoculation for several local and imported soybean varieties used in this study. Plants were harvested at 20 days after inoculation. Number of nodules were counted, fresh weight of nodules and shoot were determined. S. Fredii J-TGS50 and S. Fredii USDA 192, USDA 201, USDA 205, USDA 206, USDA 217 were found different in their symbiotic properties. S. Fredii J-TGS50 formed nodules on same imported soybean. While there were no nodules obtained from the plant inoculated with S. Fredii USDA 192, USDA 201, USDA 205, USDA 206, USDA 217. S. Fredii J-TGS50 and recommended B. Japonicum USDA 110 formed nodule on several local soybean varieties. There was no differences between those two bacteria either in nodulation efficiency or in the effectiveness of the formed nodules. Results of this study can be concluded that S. Fredii, J-TGS50 is a native to Indonesian soil and it is a promising soybean nodule forming bacteria in Indonesia. Using indigenous bacteria is valuable. Since they are mostly more tolerant and adaptable than the introduced ones. An important aspect for the success of Biological Nitrogen Fixation (BNF) is insight in the structure of indigenous soybean rhizobia populations. Study on the biodiversity of soybean rhizobia was important conducted. (author)

  10. Crystallization, preliminary X-ray diffraction and structure solution of MosA, a dihydrodipicolinate synthase from Sinorhizobium meliloti L5-30

    International Nuclear Information System (INIS)

    Leduc, Yvonne A.; Phenix, Christopher P.; Puttick, Jennifer; Nienaber, Kurt; Palmer, David R. J.; Delbaere, Louis T. J.

    2005-01-01

    MosA from S. meliloti L5-30 has been crystallized in solution with pyruvate and the 2.3 Å resolution structure has been solved by molecular replacement using E. coli dihydrodipicolinate synthase as the model. The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Å resolution using synchrotron radiation and belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Å

  11. The succinoglycan endoglycanase encoded by exoK is required for efficient symbiosis of Sinorhizobium meliloti 1021 with the host plants Medicago truncatula and Medicago sativa (Alfalfa).

    Science.gov (United States)

    Mendis, Hajeewaka C; Queiroux, Clothilde; Brewer, Tess E; Davis, Olivia M; Washburn, Brian K; Jones, Kathryn M

    2013-09-01

    The acidic polysaccharide succinoglycan produced by the nitrogen-fixing rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and to efficiently invade the host plant M. sativa (alfalfa). The β-glucanase enzyme encoded by exoK has previously been demonstrated to cleave succinoglycan and participate in producing the low molecular weight form of this polysaccharide. Here, we show that exoK is required for efficient S. meliloti invasion of both M. truncatula and alfalfa. Deletion mutants of exoK have a substantial reduction in symbiotic productivity on both of these plant hosts. Insertion mutants of exoK have an even less productive symbiosis than the deletion mutants with the host M. truncatula that is caused by a secondary effect of the insertion itself, and may be due to a polar effect on the expression of the downstream exoLAMON genes.

  12. PhoU Allows Rapid Adaptation to High Phosphate Concentrations by Modulating PstSCAB Transport Rate in Sinorhizobium meliloti.

    Science.gov (United States)

    diCenzo, George C; Sharthiya, Harsh; Nanda, Anish; Zamani, Maryam; Finan, Turlough M

    2017-09-15

    Maintenance of cellular phosphate homeostasis is essential for cellular life. The PhoU protein has emerged as a key regulator of this process in bacteria, and it is suggested to modulate phosphate import by PstSCAB and control activation of the phosphate limitation response by the PhoR-PhoB two-component system. However, a proper understanding of PhoU has remained elusive due to numerous complications of mutating phoU , including loss of viability and the genetic instability of the mutants. Here, we developed two sets of strains of Sinorhizobium meliloti that overcame these limitations and allowed a more detailed and comprehensive analysis of the biological and molecular activities of PhoU. The data showed that phoU cannot be deleted in the presence of phosphate unless PstSCAB is inactivated also. However, phoU deletions were readily recovered in phosphate-free media, and characterization of these mutants revealed that addition of phosphate to the environment resulted in toxic levels of PstSCAB-mediated phosphate accumulation. Phosphate uptake experiments indicated that PhoU significantly decreased the PstSCAB transport rate specifically in phosphate-replete cells but not in phosphate-starved cells and that PhoU could rapidly respond to elevated environmental phosphate concentrations and decrease the PstSCAB transport rate. Site-directed mutagenesis results suggested that the ability of PhoU to respond to phosphate levels was independent of the conformation of the PstSCAB transporter. Additionally, PhoU-PhoU and PhoU-PhoR interactions were detected using a bacterial two-hybrid screen. We propose that PhoU modulates PstSCAB and PhoR-PhoB in response to local, internal fluctuations in phosphate concentrations resulting from PstSCAB-mediated phosphate import. IMPORTANCE Correct maintenance of cellular phosphate homeostasis is critical in all kingdoms of life and in bacteria involves the PhoU protein. This work provides novel insights into the role of the Sinorhizobium

  13. Nitrate reduction associated with respiration in Sinorhizobium meliloti 2011 is performed by a membrane-bound molybdoenzyme.

    Science.gov (United States)

    Ferroni, Felix M; Rivas, María G; Rizzi, Alberto C; Lucca, María E; Perotti, Nora I; Brondino, Carlos D

    2011-10-01

    The purification and biochemical characterization of the respiratory membrane-bound nitrate reductase from Sinorhizobium meliloti 2011 (Sm NR) is reported together with the optimal conditions for cell growth and enzyme production. The best biomass yield was obtained under aerobic conditions in a fed-batch system using Luria-Bertani medium with glucose as carbon source. The highest level of Sm NR production was achieved using microaerobic conditions with the medium supplemented with both nitrate and nitrite. Sm NR is a mononuclear Mo-protein belonging to the DMSO reductase family isolated as a heterodimeric enzyme containing two subunits of 118 and 45 kDa. Protein characterization by mass spectrometry showed homology with respiratory nitrate reductases. UV-Vis spectra of as-isolated and dithionite reduced Sm NR showed characteristic absorption bands of iron-sulfur and heme centers. Kinetic studies indicate that Sm NR follows a Michaelis-Menten mechanism (K (m) = 97 ± 11 μM, V = 9.4 ± 0.5 μM min(-1), and k (cat) = 12.1 ± 0.6 s(-1)) and is inhibited by azide, chlorate, and cyanide with mixed inhibition patterns. Physiological and kinetic studies indicate that molybdenum is essential for NR activity and that replacement of this metal for tungsten inhibits the enzyme. Although no narGHI gene cluster has been annotated in the genome of rhizobia, the biochemical characterization indicates that Sm NR is a Mo-containing NR enzyme with molecular organization similar to NarGHI.

  14. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation.

    Science.gov (United States)

    Saramago, Margarida; Peregrina, Alexandra; Robledo, Marta; Matos, Rute G; Hilker, Rolf; Serrania, Javier; Becker, Anke; Arraiano, Cecilia M; Jiménez-Zurdo, José I

    2017-02-17

    Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.

  15. [Subcloning and sequencing of DNA fragment related to salt tolerance in Sinorhizobium meliloti 042B].

    Science.gov (United States)

    Ge, S; Fan, Z; Chen, X; Yang, S

    2001-02-01

    A 4 kb ClaI DNA fragment related to salt tolerance from S. meliloti 042B was digested by HindIII down 2.4 kb fragment, and a 1.6 kb ClaII-HindIII fragment was retained on plasmid pML122. Then, the 2.4 kb DNA fragment was ligated with plasmid pBBR1-MCS2, and the recombinant plasmid was transformed to E. coli DH5 alpha, and transformant GS2 was obtained. Three-parental mating experiments were carried out with transformant GS2 as donor, salt sensitive strains GZ17 as recipient and pRK2013 as helper plasmid, then the transconjugant GG2 was selected on FY plates containing kanamycin and 0.4 mol/L NaCl. The remaining DNA fragment was self ligated with pML122 and then transformed into E. coli S17-1 and transformat GS0 was obtained. Two-parental mating experiment was carried out with transformant GS0 as donor and salt sensitive strain GZ17 as recipient, but no transconjugant was obtained on the FY plates. Then, the 2.4 kb HindIII DNA fragment was ligated into sequencing vector pGEM-7Zf(+) for sequencing. The result of sequencing and analysis showed that the 2.4 kb DNA fragment contained three ORFs. According to the result of sequencing, further subcloning was conducted and 1.9 kb HindIII-Sac II DNA fragment related to salt tolerance was obtained.

  16. Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti.

    Science.gov (United States)

    D'Alessio, Maya; Nordeste, Ricardo; Doxey, Andrew C; Charles, Trevor C

    2017-01-01

    Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti , we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis ( phbA , phbB , phbAB , and phbC ), PHB degradation ( bdhA , phaZ , and acsA2 ), and glycogen synthesis ( glgA1 ). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes. IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to

  17. Phenotypic and molecular characterization of Sinorhizobium meliloti strains isolated from the roots of Medicago sativa in Iran

    Directory of Open Access Journals (Sweden)

    Mahboobeh Nakhaei Moghaddam

    2017-12-01

    Full Text Available Introduction: The Rhizobium-legume interaction leads to biological nitrogen-fixation and increases nitrogen of soil. The aim of this study was to characterize the properties of Sinorhizobium isolates from the roots of alfalfa plantsin Iran. Materials and methods: Bacteria were isolated in yeast extract mannitol Agar and confirmed by plant infection test. After evaluation from the point of morphological and biochemical properties, a fragment of 16S rDNA gene with a size of approximately 1500 base pair was amplified using fD1 and rD1 primers. PCR (polymerase chain reaction products were analyzed for digestion pattern by Taq1 endonuclease. Results: 63 bacteria were isolated from homogenized nodules. 42 isolates generated nodules in three replicates in infection test. Of the 42 isolates 8, were resistant to salinity. Seven isolates had better growth than others at pH 4. All isolates were resistant to CuCl2 (0.5 mmol, CdCl2 (0.65 mmol, MnSO4 (0.75 and 1.5 mmol and ZnSO4 (0.125 mmol. Isolates S3Q and S22K were more resistant to salinity, acidity, temperature and heavy metals stresses. PCR products of all bacteria had the same restricted profile after digestion by Taq1 nuclease. Discussion and conclusion: The results showed that among isolated bacteria, there were some differences in the resistance to salinity, acidity, temperature and heavy metals stresses.  Identification of native strains of rhizobia, especially strains resistant to salinity, temperature, heavy metals and acidity could be valuable due to their potentiality for using biological fertilizers in harsh conditions.

  18. The genome, proteome and phylogenetic analysis of Sinorhizobium meliloti phage ΦM12, the founder of a new group of T4-superfamily phages.

    Science.gov (United States)

    Brewer, Tess E; Stroupe, M Elizabeth; Jones, Kathryn M

    2014-02-01

    Phage ΦM12 is an important transducing phage of the nitrogen-fixing rhizobial bacterium Sinorhizobium meliloti. Here we report the genome, phylogenetic analysis, and proteome of ΦM12, the first report of the genome and proteome of a rhizobium-infecting T4-superfamily phage. The structural genes of ΦM12 are most similar to T4-superfamily phages of cyanobacteria. ΦM12 is the first reported T4-superfamily phage to lack genes encoding class I ribonucleotide reductase (RNR) and exonuclease dexA, and to possess a class II coenzyme B12-dependent RNR. ΦM12's novel collection of genes establishes it as the founder of a new group of T4-superfamily phages, fusing features of cyanophages and phages of enteric bacteria. © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Characterization of a partner switching system regulating c-di-GMP levels in Sinorhizobium meliloti. Implication in the synthesis of a novel exopolysaccharide

    OpenAIRE

    Baena Ropero, Irene

    2016-01-01

    Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 04-02-2016 Esta tesis tiene embargado el acceso al texto completo hasta el 04-08-2017 Sinorhizobium meliloti produce un β-D-glucano de enlaces alternos (1→3) (1→4) (ML β-glucano) en respuesta a altos niveles de diguanilato cíclico (di-GMP-c). Dos proteínas, BgsB y BgsA, son las responsables de la síntesis, siendo BgsA la glucano sintasa que sensa dichos ni...

  20. Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    E. V. Karaushu

    2015-01-01

    Full Text Available Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1. Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum.

  1. Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

    Science.gov (United States)

    Karaushu, E V; Lazebnaya, I V; Kravzova, T R; Vorobey, N A; Lazebny, O E; Kiriziy, D A; Olkhovich, O P; Taran, N Yu; Kots, S Ya; Popova, A A; Omarova, E; Koksharova, O A

    2015-01-01

    Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH) gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1). Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum.

  2. Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid.

    Science.gov (United States)

    Johnson, Matthew C; Tatum, Kelsey B; Lynn, Jason S; Brewer, Tess E; Lu, Stephen; Washburn, Brian K; Stroupe, M Elizabeth; Jones, Kathryn M

    2015-11-01

    Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the Sinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relative Rhizobium phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like S. meliloti phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and S. meliloti phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide. Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail

  3. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

    Science.gov (United States)

    Draghi, W O; Del Papa, M F; Hellweg, C; Watt, S A; Watt, T F; Barsch, A; Lozano, M J; Lagares, A; Salas, M E; López, J L; Albicoro, F J; Nilsson, J F; Torres Tejerizo, G A; Luna, M F; Pistorio, M; Boiardi, J L; Pühler, A; Weidner, S; Niehaus, K; Lagares, A

    2016-07-11

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

  4. Production of nodulation factors by Rhizobium meliloti: fermentation, purification and characterization of glycolipids.

    Science.gov (United States)

    Kohring, B; Baier, R; Niehaus, K; Pühler, A; Flaschel, E

    1997-12-01

    Lipooligosaccharides, synthesized by soil bacteria of the genera Rhizobium, are known to have multifunctional effects on a wide variety of plants as signal substances in symbiosis initiation, cell response elicitation and growth regulation. These so called nodulation (Nod-) factors represent interesting biotechnological products with respect to fundamental studies of symbiotic interactions as well as for potential applications. Therefore, a batch fermentation process on a scale of 30 l has been developed by means of the Rhizobium meliloti strain R.m. 1021 (pEK327) strongly overexpressing the genes for the synthesis of Nod factors. Induction by the flavone luteolin led to growth associated production of the lipooligosaccharides. Ultrafiltration was used for separating the biomass from the filtrate containing the extracellular Nod factors. Simultaneously, ultrafiltration reduced the amount of lipophilic substances, which would otherwise interfere with processes downstream. The second separation step consisted in adsorption on XAD-2, a nonspecific hydrophobic adsorptive resin. Adsorption of Nod factors was carried out by batch operation of a stirred tank. Desorption was performed by elution with methanol in a fixed bed column. A semi-preparative reversed phase HPLC (Polygoprep 100-30 C18) was chosen as the final purification step. The Nod factors were obtained after evaporation and lyophilization. Thus, about 600 mg of Nod factors were produced from 20 l of fermentation broth. The Nod factors produced by Rhizobium meliloti R.m. 1021 (pEK327) were identified by liquid secondary ion mass spectrometry and by reversed-phase HPLC as fluorescent derivatives of 2-aminobenzamide. The biological activity of the products was demonstrated by means of the root hair deformation (HAD-) assay.

  5. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis

    NARCIS (Netherlands)

    Wang, D.; Griffitts, J.; Starker, C.; Fedorova, E.; Limpens, E.H.M.; Ivanov, S.E.; Bisseling, T.; Long, S.

    2010-01-01

    The nitrogen-fixing symbiosis between Sinorhizobium meliloti and its leguminous host plant Medicago truncatula occurs in a specialized root organ called the nodule. Bacteria that are released into plant cells are surrounded by a unique plant membrane compartment termed a symbiosome. We found that in

  6. Pseudoazurin from Sinorhizobium meliloti as an electron donor to copper-containing nitrite reductase: influence of the redox partner on the reduction potentials of the enzyme copper centers.

    Science.gov (United States)

    Ferroni, Félix M; Marangon, Jacopo; Neuman, Nicolás I; Cristaldi, Julio C; Brambilla, Silvina M; Guerrero, Sergio A; Rivas, María G; Rizzi, Alberto C; Brondino, Carlos D

    2014-08-01

    Pseudoazurin (Paz) is the physiological electron donor to copper-containing nitrite reductase (Nir), which catalyzes the reduction of NO2 (-) to NO. The Nir reaction mechanism involves the reduction of the type 1 (T1) copper electron transfer center by the external physiological electron donor, intramolecular electron transfer from the T1 copper center to the T2 copper center, and nitrite reduction at the type 2 (T2) copper catalytic center. We report the cloning, expression, and characterization of Paz from Sinorhizobium meliloti 2011 (SmPaz), the ability of SmPaz to act as an electron donor partner of S. meliloti 2011 Nir (SmNir), and the redox properties of the metal centers involved in the electron transfer chain. Gel filtration chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis together with UV-vis and EPR spectroscopies revealed that as-purified SmPaz is a mononuclear copper-containing protein that has a T1 copper site in a highly distorted tetrahedral geometry. The SmPaz/SmNir interaction investigated electrochemically showed that SmPaz serves as an efficient electron donor to SmNir. The formal reduction potentials of the T1 copper center in SmPaz and the T1 and T2 copper centers in SmNir, evaluated by cyclic voltammetry and by UV-vis- and EPR-mediated potentiometric titrations, are against an efficient Paz T1 center to Nir T1 center to Nir T2 center electron transfer. EPR experiments proved that as a result of the SmPaz/SmNir interaction in the presence of nitrite, the order of the reduction potentials of SmNir reversed, in line with T1 center to T2 center electron transfer being thermodynamically more favorable.

  7. Sinorhizobium meliloti sigma factors RpoE1 and RpoE4 are activated in stationary phase in response to sulfite.

    Directory of Open Access Journals (Sweden)

    Bénédicte Bastiat

    Full Text Available Rhizobia are soil bacteria able to establish a nitrogen-fixing symbiosis with legume plants. Both in soil and in planta, rhizobia spend non-growing periods resembling the stationary phase of in vitro-cultured bacteria. The primary objective of this work was to better characterize gene regulation in this biologically relevant growth stage in Sinorhizobium meliloti. By a tap-tag/mass spectrometry approach, we identified five sigma factors co-purifying with the RNA polymerase in stationary phase: the general stress response regulator RpoE2, the heat shock sigma factor RpoH2, and three extra-cytoplasmic function sigma factors (RpoE1, RpoE3 and RpoE4 belonging to the poorly characterized ECF26 subgroup. We then showed that RpoE1 and RpoE4 i are activated upon metabolism of sulfite-generating compounds (thiosulfate and taurine, ii display overlapping regulatory activities, iii govern a dedicated sulfite response by controlling expression of the sulfite dehydrogenase SorT, iv are activated in stationary phase, likely as a result of endogenous sulfite generation during bacterial growth. We showed that SorT is required for optimal growth of S. meliloti in the presence of sulfite, suggesting that the response governed by RpoE1 and RpoE4 may be advantageous for bacteria in stationary phase either by providing a sulfite detoxification function or by contributing to energy production through sulfite respiration. This paper therefore reports the first characterization of ECF26 sigma factors, the first description of sigma factors involved in control of sulphur metabolism, and the first indication that endogenous sulfite may act as a signal for regulation of gene expression upon entry of bacteria in stationary phase.

  8. The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain

    Directory of Open Access Journals (Sweden)

    Brom Susana

    2011-06-01

    Full Text Available Abstract Background Bean-nodulating Rhizobium etli originated in Mesoamerica, while soybean-nodulating Sinorhizobium fredii evolved in East Asia. S. fredii strains, such as GR64, have been isolated from bean nodules in Spain, suggesting the occurrence of conjugative transfer events between introduced and native strains. In R. etli CFN42, transfer of the symbiotic plasmid (pRet42d requires cointegration with the endogenous self-transmissible plasmid pRet42a. Aiming at further understanding the generation of diversity among bean nodulating strains, we analyzed the plasmids of S. fredii GR64: pSfr64a and pSfr64b (symbiotic plasmid. Results The conjugative transfer of the plasmids of strain GR64 was analyzed. Plasmid pSfr64a was self-transmissible, and required for transfer of the symbiotic plasmid. We sequenced pSfr64a, finding 166 ORFs. pSfr64a showed three large segments of different evolutionary origins; the first one presented 38 ORFs that were highly similar to genes located on the chromosome of Sinorhizobium strain NGR234; the second one harbored 51 ORFs with highest similarity to genes from pRet42d, including the replication, but not the symbiosis genes. Accordingly, pSfr64a was incompatible with the R. etli CFN42 symbiotic plasmid, but did not contribute to symbiosis. The third segment contained 36 ORFs with highest similarity to genes localized on pRet42a, 20 of them involved in conjugative transfer. Plasmid pRet42a was unable to substitute pSfr64a for induction of pSym transfer, and its own transfer was significantly diminished in GR64 background. The symbiotic plasmid pSfr64b was found to differ from typical R. etli symbiotic plasmids. Conclusions S. fredii GR64 contains a chimeric transmissible plasmid, with segments from two R. etli plasmids and a S. fredii chromosome, and a symbiotic plasmid different from the one usually found in R. etli bv phaseoli. We infer that these plasmids originated through the transfer of a symbiotic

  9. Characterization of genes for synthesis and catabolism of a new rhizopine induced in nodules by Rhizobium meliloti Rm220-3: extension of the rhizopine concept.

    OpenAIRE

    Saint, C P; Wexler, M; Murphy, P J; Tempé, J; Tate, M E; Murphy, P J

    1993-01-01

    Rhizopines are selective growth substrates synthesized in nodules only by strains of rhizobia capable of their catabolism. We report the isolation and study of genes for the synthesis and catabolism of a new rhizopine, scyllo-inosamine (sIa), from alfalfa nodules induced by Rhizobium meliloti Rm220-3. This compound is similar in structure to the previously described rhizopine 3-O-methyl-scyllo-inosamine from R. meliloti L5-30 (P.J. Murphy, N. Heycke, Z. Banfalvi, M.E. Tate, F.J. de Bruijn, A....

  10. Extended region of nodulation genes in Rhizobium meliloti 1021. II. Nucleotide sequence, transcription start sites and protein products

    International Nuclear Information System (INIS)

    Fisher, R.F.; Swanson, J.A.; Mulligan, J.T.; Long, S.R.

    1987-01-01

    The authors have established the DNA sequence and analyzed the transcription and translation products of a series of putative nodulation (nod) genes in Rhizobium meliloti strain 1021. Four loci have been designated nodF, nodE, nodG and nodH. The correlation of transposon insertion positions with phenotypes and open reading frames was confirmed by sequencing the insertion junctions of the transposons. The protein products of these nod genes were visualized by in vitro expression of cloned DNA segments in a R. meliloti transcription-translation system. In addition, the sequence for nodG was substantiated by creating translational fusions in all three reading frames at several points in the sequence; the resulting fusions were expressed in vitro in both E. coli and R. meliloti transcription-translation systems. A DNA segment bearing several open reading frames downstream of nodG corresponds to the putative nod gene mutated in strain nod-216. The transcription start sites of nodF and nodH were mapped by primer extension of RNA from cells induced with the plant flavone, luteolin. Initiation of transcription occurs approximately 25 bp downstream from the conserved sequence designated the nod box, suggesting that this conserved sequence acts as an upstream regulator of inducible nod gene expression. Its distance from the transcription start site is more suggestive of an activator binding site rather than an RNA polymerase binding site

  11. Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome.

    Science.gov (United States)

    Johnson, Matthew C; Sena-Velez, Marta; Washburn, Brian K; Platt, Georgia N; Lu, Stephen; Brewer, Tess E; Lynn, Jason S; Stroupe, M Elizabeth; Jones, Kathryn M

    2017-12-01

    Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7Å-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus ΦM5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, ΦM5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail. Nonetheless, this group is phylogenetically quite distinct from Podoviruses of the well-characterized T7, P22, and epsilon 15 supergroups. Structurally, a distinct bridge of density that appears unique to ΦM5 reaches down the body of the coat protein to the extended loop that interacts with the next monomer in a hexamer, perhaps stabilizing the mature capsid. Further, the predicted tail fibers of ΦM5 are quite different from those of enteric bacteria phages, but have domains in common with other rhizophages. Genomically, ΦM5 is highly mosaic. The ΦM5 genome is 44,005bp with 357bp direct terminal repeats (DTRs) and 58 unique ORFs. Surprisingly, the capsid structural module, the tail module, the DNA-packaging terminase, the DNA replication module and the integrase each appear to be from a different lineage. One of the most unusual features of ΦM5 is its terminase whose large subunit is quite different from previously-described short-DTR-generating packaging machines and does not fit into any of the established phylogenetic groups. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. A novel RNA-binding peptide regulates the establishment of the Medicago truncatula-Sinorhizobium meliloti nitrogen-fixing symbiosis.

    Science.gov (United States)

    Laporte, Philippe; Satiat-Jeunemaître, Béatrice; Velasco, Isabel; Csorba, Tibor; Van de Velde, Willem; Campalans, Anna; Burgyan, Joszef; Arevalo-Rodriguez, Miguel; Crespi, Martin

    2010-04-01

    Plants use a variety of small peptides for cell to cell communication during growth and development. Leguminous plants are characterized by their ability to develop nitrogen-fixing nodules via an interaction with symbiotic bacteria. During nodule organogenesis, several so-called nodulin genes are induced, including large families that encode small peptides. Using a three-hybrid approach in yeast cells, we identified two new small nodulins, MtSNARP1 and MtSNARP2 (for small nodulin acidic RNA-binding protein), which interact with the RNA of MtENOD40, an early induced nodulin gene showing conserved RNA secondary structures. The SNARPs are acidic peptides showing single-stranded RNA-binding activity in vitro and are encoded by a small gene family in Medicago truncatula. These peptides exhibit two new conserved motifs and a putative signal peptide that redirects a GFP fusion to the endoplasmic reticulum both in protoplasts and during symbiosis, suggesting they are secreted. MtSNARP2 is expressed in the differentiating region of the nodule together with several early nodulin genes. MtSNARP2 RNA interference (RNAi) transgenic roots showed aberrant early senescent nodules where differentiated bacteroids degenerate rapidly. Hence, a functional symbiotic interaction may be regulated by secreted RNA-binding peptides.

  13. High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala.

    Science.gov (United States)

    Li, Yan; Tian, Chang Fu; Chen, Wen Feng; Wang, Lei; Sui, Xin Hua; Chen, Wen Xin

    2013-01-01

    The rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. Sinorhizobium sp. NGR234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. Here, we presented a high-resolution RNA-seq transcriptomic analysis of NGR234 bacteroids in indeterminate nodules of Leucaena leucocephala and determinate nodules of Vigna unguiculata. In contrast to exponentially growing free-living bacteria, non-growing bacteroids from both legumes recruited several common cellular functions such as cbb3 oxidase, thiamine biosynthesis, nitrate reduction pathway (NO-producing), succinate metabolism, PHB (poly-3-hydroxybutyrate) biosynthesis and phosphate/phosphonate transporters. However, different transcription profiles between bacteroids from two legumes were also uncovered for genes involved in the biosynthesis of exopolysaccharides, lipopolysaccharides, T3SS (type three secretion system) and effector proteins, cytochrome bd ubiquinol oxidase, PQQ (pyrroloquinoline quinone), cytochrome c550, pseudoazurin, biotin, phasins and glycolate oxidase, and in the metabolism of glutamate and phenylalanine. Noteworthy were the distinct expression patterns of genes encoding phasins, which are thought to be involved in regulating the surface/volume ratio of PHB granules. These patterns are in good agreement with the observed granule size difference between bacteroids from L. leucocephala and V. unguiculata.

  14. High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala.

    Directory of Open Access Journals (Sweden)

    Yan Li

    Full Text Available The rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. Sinorhizobium sp. NGR234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. Here, we presented a high-resolution RNA-seq transcriptomic analysis of NGR234 bacteroids in indeterminate nodules of Leucaena leucocephala and determinate nodules of Vigna unguiculata. In contrast to exponentially growing free-living bacteria, non-growing bacteroids from both legumes recruited several common cellular functions such as cbb3 oxidase, thiamine biosynthesis, nitrate reduction pathway (NO-producing, succinate metabolism, PHB (poly-3-hydroxybutyrate biosynthesis and phosphate/phosphonate transporters. However, different transcription profiles between bacteroids from two legumes were also uncovered for genes involved in the biosynthesis of exopolysaccharides, lipopolysaccharides, T3SS (type three secretion system and effector proteins, cytochrome bd ubiquinol oxidase, PQQ (pyrroloquinoline quinone, cytochrome c550, pseudoazurin, biotin, phasins and glycolate oxidase, and in the metabolism of glutamate and phenylalanine. Noteworthy were the distinct expression patterns of genes encoding phasins, which are thought to be involved in regulating the surface/volume ratio of PHB granules. These patterns are in good agreement with the observed granule size difference between bacteroids from L. leucocephala and V. unguiculata.

  15. Overexpression of flavodoxin in bacteroids induces changes in antioxidant metabolism leading to delayed senescence and starch accumulation in alfalfa root nodules.

    Science.gov (United States)

    Redondo, Francisco J; de la Peña, Teodoro Coba; Morcillo, César N; Lucas, M Mercedes; Pueyo, José J

    2009-02-01

    Sinorhizobium meliloti cells were engineered to overexpress Anabaena variabilis flavodoxin, a protein that is involved in the response to oxidative stress. Nodule natural senescence was characterized in alfalfa (Medicago sativa) plants nodulated by the flavodoxin-overexpressing rhizobia or the corresponding control bacteria. The decline of nitrogenase activity and the nodule structural and ultrastructural alterations that are associated with nodule senescence were significantly delayed in flavodoxin-expressing nodules. Substantial changes in nodule antioxidant metabolism, involving antioxidant enzymes and ascorbate-glutathione cycle enzymes and metabolites, were detected in flavodoxin-containing nodules. Lipid peroxidation was also significantly lower in flavodoxin-expressing nodules than in control nodules. The observed amelioration of the oxidative balance suggests that the delay in nodule senescence was most likely due to a role of the protein in reactive oxygen species detoxification. Flavodoxin overexpression also led to high starch accumulation in nodules, without reduction of the nitrogen-fixing activity.

  16. Possible Role of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity of Sinorhizobium sp. BL3 on Symbiosis with Mung Bean and Determinate Nodule Senescence

    Science.gov (United States)

    Tittabutr, Panlada; Sripakdi, Sudarat; Boonkerd, Nantakorn; Tanthanuch, Waraporn; Minamisawa, Kiwamu; Teaumroong, Neung

    2015-01-01

    Sinorhizobium sp. BL3 forms symbiotic interactions with mung bean (Vigna radiata) and contains lrpL-acdS genes, which encode the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme that cleaves ACC, a precursor of plant ethylene synthesis. Since ethylene interferes with nodule formation in some legumes and plays a role in senescence in plant cells, BL3-enhancing ACC deaminase activity (BL3+) and defective mutant (BL3−) strains were constructed in order to investigate the effects of this enzyme on symbiosis and nodule senescence. Nodulation competitiveness was weaker in BL3− than in the wild-type, but was stronger in BL3+. The inoculation of BL3− into mung bean resulted in less plant growth, a lower nodule dry weight, and smaller nodule number than those in the wild-type, whereas the inoculation of BL3+ had no marked effects. However, similar nitrogenase activity was observed with all treatments; it was strongly detected 3 weeks after the inoculation and gradually declined with time, indicating senescence. The rate of plant nodulation by BL3+ increased in a time-dependent manner. Nodules occupied by BL3− formed smaller symbiosomes, and bacteroid degradation was more prominent than that in the wild-type 7 weeks after the inoculation. Changes in biochemical molecules during nodulation were tracked by Fourier Transform Infrared (FT-IR) microspectroscopy, and the results obtained confirmed that aging processes differed in nodules occupied by BL3 and BL3−. This is the first study to show the possible role of ACC deaminase activity in senescence in determinate nodules. Our results suggest that an increase in ACC deaminase activity in this strain does not extend the lifespan of nodules, whereas the lack of this activity may accelerate nodule senescence. PMID:26657304

  17. Alfalfa nodules elicited by a flavodoxin-overexpressing Ensifer meliloti strain display nitrogen-fixing activity with enhanced tolerance to salinity stress.

    Science.gov (United States)

    Redondo, Francisco J; Coba de la Peña, Teodoro; Lucas, M Mercedes; Pueyo, José J

    2012-12-01

    Nitrogen fixation by legumes is very sensitive to salinity stress, which can severely reduce the productivity of legume crops and their soil-enriching capacity. Salinity is known to cause oxidative stress in the nodule by generating reactive oxygen species (ROS). Flavodoxins are involved in the response to oxidative stress in bacteria and cyanobacteria. Prevention of ROS production by flavodoxin overexpression in bacteroids might lead to a protective effect on nodule functioning under salinity stress. Tolerance to salinity stress was evaluated in alfalfa nodules elicited by an Ensifer meliloti strain that overexpressed a cyanobacterial flavodoxin compared with nodules produced by the wild-type bacteria. Nitrogen fixation, antioxidant and carbon metabolism enzyme activities were determined. The decline in nitrogenase activity associated to salinity stress was significantly less in flavodoxin-expressing than in wild-type nodules. We detected small but significant changes in nodule antioxidant metabolism involving the ascorbate-glutathione cycle enzymes and metabolites, as well as differences in activity of the carbon metabolism enzyme sucrose synthase, and an atypical starch accumulation pattern in flavodoxin-containing nodules. Salt-induced structural and ultrastructural alterations were examined in detail in alfalfa wild-type nodules by light and electron microscopy and compared to flavodoxin-containing nodules. Flavodoxin reduced salt-induced structural damage, which primarily affected young infected tissues and not fully differentiated bacteroids. The results indicate that overexpression of flavodoxin in bacteroids has a protective effect on the function and structure of alfalfa nodules subjected to salinity stress conditions. Putative protection mechanisms are discussed.

  18. Overexpression, purification, and biochemical and spectroscopic characterization of copper-containing nitrite reductase from Sinorhizobium meliloti 2011. Study of the interaction of the catalytic copper center with nitrite and NO.

    Science.gov (United States)

    Ferroni, Félix M; Guerrero, Sergio A; Rizzi, Alberto C; Brondino, Carlos D

    2012-09-01

    The entire nirK gene coding for a putative copper-nitrite reductase (Nir) from Sinorhizobium meliloti 2011 (Sm) was cloned and overexpressed heterologously in Escherichia coli for the first time. The spectroscopic and molecular properties of the enzyme indicate that SmNir is a green Nir with homotrimeric structure (42.5 kDa/subunit) containing two copper atoms per monomer, one of type 1 and the other of type 2. SmNir follows a Michaelis-Menten mechanism and is inhibited by cyanide. EPR spectra of the as-purified enzyme exhibit two magnetically different components associated with type 1 and type 2 copper centers in a 1:1 ratio. EPR characterization of the copper species obtained upon interaction of SmNir with nitrite, and catalytically-generated and exogenous NO reveals the formation of a Cu-NO EPR active species not detected before in closely related Nirs. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. La simbiosis fijadora de nitrógeno Sinorhizobium meliloti-alfalfa: aproximaciones ómicas aplicadas a la identificación y caracterización de determinantes genéticos del rizobio asociados a la colonización temprana de la raíz de alfalfa (Medicago sativa)

    OpenAIRE

    Salas, María Eugenia

    2015-01-01

    Sinorhizobium meliloti es una α-proteobacteria capaz de establecer asociaciones simbióticas con plantas de los géneros Medicago, Melilotus y Trigonella. Esta asociación es el resultado de un complejo diálogo molecular entre los simbiontes, que se diferencian a lo largo de la interacción para dar lugar a un nuevo órgano en las raíces de las plantas, el nódulo fijador de nitrógeno. El nicho simbiótico accesible a los rizobios está naturalmente limitado, y resulta ocupado por aquellas cepas que ...

  20. Estudio del efecto de la interacción entre aumento de CO₂, temperatura y simbiosis con diferentes cepas de Sinorhizobium meliloti en la fotosíntesis, fijación de N₂ y calidad de la alfalfa (Medicago sativa L. cv Aragón)

    OpenAIRE

    Sanz, A. (Álvaro); Irigoyen, J.J. (Juan José); Erice, G. (Gorka)

    2012-01-01

    El objetivo general del estudio realizado, fue investigar la respuesta de plantas de alfalfa inoculadas con diferentes cepas de Sinorhizobium meliloti (102F78, 102F34 y 1032GMI) frente al aumento de CO₂ y temperatura. Los objetivos parciales planteados y desarrollados en los distintos capítulos de la memoria han sido: - Capítulo 1: Comprobar si plantas de alfalfa exclusivamente fijadoras de N₂ inoculadas con la cepa 102F78 tienen un aporte deficiente de N desde el nódulo que limita la res...

  1. Metabolite profiles of nodulated alfalfa plants indicate that distinct stages of nodule organogenesis are accompanied by global physiological adaptations.

    Science.gov (United States)

    Barsch, Aiko; Tellström, Verena; Patschkowski, Thomas; Küster, Helge; Niehaus, Karsten

    2006-09-01

    An effective symbiosis between Sinorhizobium meliloti and its host plant Medicago sativa is dependent on a balanced physiological interaction enabling the microsymbiont to fix atmospheric nitrogen. Maintenance of the symbiotic interaction is regulated by still poorly understood control mechanisms. A first step toward a better understanding of nodule metabolism was the determination of characteristic metabolites for alfalfa root nodules. Furthermore, nodules arrested at different developmental stages were analyzed in order to address metabolic changes induced during the progression of nodule formation. Metabolite profiles of bacteroid-free pseudonodule extracts indicated that early nodule developmental processes are accompanied by photosynthate translocation but no massive organic acid formation. To determine metabolic adaptations induced by the presence of nonfixing bacteroids, nodules induced by mutant S. meliloti strains lacking the nitrogenase protein were analyzed. The bacteroids are unable to provide ammonium to the host plant, which is metabolically reflected by reduced levels of characteristic amino acids involved in ammonium fixation. Elevated levels of starch and sugars in Fix(-) nodules provide strong evidence that plant sanctions preventing a transformation from a symbiotic to a potentially parasitic interaction are not strictly realized via photosynthate supply. Instead, metabolic and gene expression data indicate that alfalfa plants react to nitrogen-fixation-deficient bacteroids with a decreased organic acid synthesis and an early induction of senescence. Noneffective symbiotic interactions resulting from plants nodulated by mutant rhizobia also are reflected in characteristic metabolic changes in leaves. These are typical for nitrogen deficiency, but also highlight metabolites potentially involved in sensing the N status.

  2. A nopA deletion mutant of Sinorhizobium fredii USDA257, a soybean symbiont, is impaired in nodulation

    Science.gov (United States)

    Sinorhizobium fredii USDA257 employs type III secretion system (T3SS) to deliver effector proteins into the host cells through filamentous surface appendages, called pili. The NopA protein is the major component of USDA257 pili. The promoter region of USDA257 nopA posses a well conserved tts box. Se...

  3. The trehalose utilization gene thuA ortholog in Mesorhizobium loti does not influence competitiveness for nodulation on Lotus spp.

    Science.gov (United States)

    Ampomah, Osei Yaw; Jensen, John Beck

    2014-03-01

    Competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. In Sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thuA or thuB influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. We have therefore investigated whether mutation in the thuA ortholog in Mesorhizobium loti MAFF303099 also leads to a similar competitive phenotype on its hosts. The results show that M. loti thuA mutant Ml7023 was symbiotically effective and was as competitive as the wild type in colonization and nodule occupancy on Lotus corniculatus and Lotus japonicus. The thuA gene in M. loti was not induced during root colonization or in the infection threads unlike in S. meliloti, despite its induction by trehalose and high osmolarity in in vitro assays.

  4. NAD(P)+-malic enzyme mutants of Sinorhizobium sp. strain NGR234, but not Azorhizobium caulinodans ORS571, maintain symbiotic N2 fixation capabilities.

    Science.gov (United States)

    Zhang, Ye; Aono, Toshihiro; Poole, Phillip; Finan, Turlough M

    2012-04-01

    C(4)-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (TCA) cycle in N(2)-fixing bacteria (bacteroids) within legume nodules. In Sinorhizobium meliloti bacteroids from alfalfa, NAD(+)-malic enzyme (DME) is required for N(2) fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. In contrast, in the pea symbiont Rhizobium leguminosarum, pyruvate synthesis occurs via either DME or a pathway catalyzed by phosphoenolpyruvate carboxykinase (PCK) and pyruvate kinase (PYK). Here we report that dme mutants of the broad-host-range Sinorhizobium sp. strain NGR234 formed nodules whose level of N(2) fixation varied from 27 to 83% (plant dry weight) of the wild-type level, depending on the host plant inoculated. NGR234 bacteroids had significant PCK activity, and while single pckA and single dme mutants fixed N(2) at reduced rates, a pckA dme double mutant had no N(2)-fixing activity (Fix(-)). Thus, NGR234 bacteroids appear to synthesize pyruvate from TCA cycle intermediates via DME or PCK pathways. These NGR234 data, together with other reports, suggested that the completely Fix(-) phenotype of S. meliloti dme mutants may be specific to the alfalfa-S. meliloti symbiosis. We therefore examined the ME-like genes azc3656 and azc0119 from Azorhizobium caulinodans, as azc3656 mutants were previously shown to form Fix(-) nodules on the tropical legume Sesbania rostrata. We found that purified AZC3656 protein is an NAD(P)(+)-malic enzyme whose activity is inhibited by acetyl-coenzyme A (acetyl-CoA) and stimulated by succinate and fumarate. Thus, whereas DME is required for symbiotic N(2) fixation in A. caulinodans and S. meliloti, in other rhizobia this activity can be bypassed via another pathway(s).

  5. Molecular Signals Controlling the Inhibition of Nodulation by Nitrate in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Giel E. van Noorden

    2016-07-01

    Full Text Available The presence of nitrogen inhibits legume nodule formation, but the mechanism of this inhibition is poorly understood. We found that 2.5 mM nitrate and above significantly inhibited nodule initiation but not root hair curling in Medicago trunatula. We analyzed protein abundance in M. truncatula roots after treatment with either 0 or 2.5 mM nitrate in the presence or absence of its symbiont Sinorhizobium meliloti after 1, 2 and 5 days following inoculation. Two-dimensional gel electrophoresis combined with mass spectrometry was used to identify 106 differentially accumulated proteins responding to nitrate addition, inoculation or time point. While flavonoid-related proteins were less abundant in the presence of nitrate, addition of Nod gene-inducing flavonoids to the Sinorhizobium culture did not rescue nodulation. Accumulation of auxin in response to rhizobia, which is also controlled by flavonoids, still occurred in the presence of nitrate, but did not localize to a nodule initiation site. Several of the changes included defense- and redox-related proteins, and visualization of reactive oxygen species indicated that their induction in root hairs following Sinorhizobium inoculation was inhibited by nitrate. In summary, the presence of nitrate appears to inhibit nodulation via multiple pathways, including changes to flavonoid metabolism, defense responses and redox changes.

  6. Denitrification by Rhizobium meliloti

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, A.

    1996-10-01

    Rhizobium meliloti strains were investigated for their denitrification activity as free-living cells and in nodules on lucerne (Medicago sativa) roots. They were also investigated for presence of nitrous oxide reductase (nos) activity and for genes using a nosZ probe derived from the Pseudomonas stutzeri. To decide whether R. meliloti strains used as inoculants contribute to the total denitrification activity in a lucerne ley, strains with different denitrifying capacities were used in field and laboratory experiments. The nitrate reduction activity of R. meliloti during anaerobic respiration was compared with that of a strain of Pseudomonas aeruginosa. A great diversity in the denitrification activity was found within strains of R. meliloti, and four of thirteen investigated strains showed an obvious denitrification activity. Two denitrifying bacteria were used as references, one strain each of Bradyrhizobium japonicum and P. aeruginosa. All but one of the R. meliloti strains hybridized to the PstI-fragment of the nosZ-gene from P. stutzeri. Two sizes of the hybridizing fragment, 5 and 7 kb, were noticed. Nos activity was only shown in three R. meliloti strains, and these were all characterized by a high denitrification activity. The potential denitrification activity was about 20, 40, and 80 times higher than the actual denitrification activity for lucerne, fallow, and grass, respectively. The potential denitrification activity was almost the same in lucerne and grass planted soils. Compared with the unplanted soil, the presence of lucerne roots in the soil increased the actual denitrification activity, while roots of both plant species, grass and lucerne, increased the potential denitrification activity in the soil. 32 refs, 7 figs, 1 tab

  7. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis.

    Science.gov (United States)

    Wang, Dong; Griffitts, Joel; Starker, Colby; Fedorova, Elena; Limpens, Erik; Ivanov, Sergey; Bisseling, Ton; Long, Sharon

    2010-02-26

    The nitrogen-fixing symbiosis between Sinorhizobium meliloti and its leguminous host plant Medicago truncatula occurs in a specialized root organ called the nodule. Bacteria that are released into plant cells are surrounded by a unique plant membrane compartment termed a symbiosome. We found that in the symbiosis-defective dnf1 mutant of M. truncatula, bacteroid and symbiosome development are blocked. We identified the DNF1 gene as encoding a subunit of a signal peptidase complex that is highly expressed in nodules. By analyzing data from whole-genome expression analysis, we propose that correct symbiosome development in M. truncatula requires the orderly secretion of protein constituents through coordinated up-regulation of a nodule-specific pathway exemplified by DNF1.

  8. Genotypic characterization of indigenous Sinorhizobium meliloti and ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    . E-mail: S.Udupa@cgiar. ... estimate biological diversity exists in the native rhizobia populations, in order to understand the ..... be considered a standard method for the identification of bacteria at the family, genus and species ...

  9. Acacia senegal and Prosopis chilensis-nodulating rhizobia Sinorhizobium arboris HAMBI 2361 and S. kostiense HAMBI 2362 produce tetra- and pentameric LCOs that are N-methylated, O-6-carbamoylated and partially sulfated.

    Science.gov (United States)

    Nowak, Petri; Soupas, Laura; Thomas-Oates, Jane; Lindström, Kristina

    2004-04-28

    Sinorhizobium arboris and S. kostiense are rhizobia that nodulate the tropical leguminous trees Acacia senegal and Prosopis chilensis. The lipochito-oligosaccharidic signalling molecules (LCOs) of S. arboris HAMBI 2361 and S. kostiense HAMBI 2362 were analyzed by mass spectrometry. The major LCOs produced by the strains were shown to be pentameric, acylated with common fatty acids, N-methylated, O-6-carbamoylated and partially sulfated, as are the LCOs characterized to date for other Acacia-nodulating rhizobia. Besides the major LCOs the two strains produced (i) tetrameric LCOs, (ii) LCOs acylated with fatty acids other than those commonly found, (iii) LCOs with only an acyl substituent and (iv) noncarbamoylated LCOs. Production of LCOs (i) to (iii) are novel among Acacia-nodulating rhizobia. The roles of the different structural characteristics of LCOs in the rhizobium-A. senegal symbiosis are discussed. Specific structural features of the LCOs are proposed to be important in the selection of effective nitrogen-fixing rhizobia by A. senegal.

  10. Genetic identification and symbiotic efficiency of Sinorhizobium ...

    African Journals Online (AJOL)

    Genetic characterization by rep-PCR and RAPD-PCR was applied to study the status of S. melitloti populations inhabiting nodules of alfalfa. Cluster analysis of rep-PCR profiles showed significant differences among S. meliloti isolates. Both methods resulted in almost identical grouping of strains. Among indigenous strains ...

  11. Malic Enzyme Cofactor and Domain Requirements for Symbiotic N2 Fixation by Sinorhizobium meliloti▿ †

    Science.gov (United States)

    Mitsch, Michael J.; Cowie, Alison; Finan, Turlough M.

    2007-01-01

    The NAD+-dependent malic enzyme (DME) and the NADP+-dependent malic enzyme (TME) of Sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid N-terminal region homologous to other malic enzymes and a 330-amino-acid C-terminal region with similarity to phosphotransacetylase enzymes (PTA). We have shown previously that dme mutants of S. meliloti fail to fix N2 (Fix−) in alfalfa root nodules, whereas tme mutants are unimpaired in their N2-fixing ability (Fix+). Here we report that the amount of DME protein in bacteroids is 10 times greater than that of TME. We therefore investigated whether increased TME activity in nodules would allow TME to function in place of DME. The tme gene was placed under the control of the dme promoter, and despite elevated levels of TME within bacteroids, no symbiotic nitrogen fixation occurred in dme mutant strains. Conversely, expression of dme from the tme promoter resulted in a large reduction in DME activity and symbiotic N2 fixation. Hence, TME cannot replace the symbiotic requirement for DME. In further experiments we investigated the DME PTA-like domain and showed that it is not required for N2 fixation. Thus, expression of a DME C-terminal deletion derivative or the Escherichia coli NAD+-dependent malic enzyme (sfcA), both of which lack the PTA-like region, restored wild-type N2 fixation to a dme mutant. Our results have defined the symbiotic requirements for malic enzyme and raise the possibility that a constant high ratio of NADPH + H+ to NADP in nitrogen-fixing bacteroids prevents TME from functioning in N2-fixing bacteroids. PMID:17071765

  12. Diversity and numbers of root-nodule bacteria (rhizobia in Polish soils

    Directory of Open Access Journals (Sweden)

    Stefan Martyniuk

    2011-01-01

    Full Text Available Using a sand pouch-plant infection method, populations of several species of root-nodule bacteria (rhizobia were enumerated in eighty soils collected throughout Poland. Rhizobium leguminosarum bv. viciae (symbionts of pea, faba bean, vetch and R. leguminosarum bv. trifolii (symbionts of clover were detected in 77 and 76 soils, respectively. Most of these soils contained moderate and high numbers of these species of the rhizobia. Symbionts of beans, R. leguminosarum bv. phaseoli, were assessed in 76 soils; of this number 15 soils had no detectable populations of bean rhizobia and in 40 soils high or moderate numbers of these bacteria were found. Bradyrhizobium sp. (Lupinus, root-nodule bacteria of lupine and serradella, were absent in 19 soils, out of 80 tested, and 34 soils were colonised by high or moderate populations of bradyrhizobia. Sinorhizobium meliloti, rhizobia nodulating alfalfa, were sparse in the examined soils; with 56 soil containing no detectable numbers of S. meliloti and only 6 soils harbouring high or moderate populations of this species. The estimated numbers of the rhizobia in the studied soils were also related to some physical and chemical properties of these soils.

  13. Nodule-enhanced expression of a sucrose phosphate synthase gene member (MsSPSA) has a role in carbon and nitrogen metabolism in the nodules of alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Aleman, Lorenzo; Ortega, Jose Luis; Martinez-Grimes, Martha; Seger, Mark; Holguin, Francisco Omar; Uribe, Diana J; Garcia-Ibilcieta, David; Sengupta-Gopalan, Champa

    2010-01-01

    Sucrose phosphate synthase (SPS) catalyzes the first step in the synthesis of sucrose in photosynthetic tissues. We characterized the expression of three different isoforms of SPS belonging to two different SPS gene families in alfalfa (Medicago sativa L.), a previously identified SPS (MsSPSA) and two novel isoforms belonging to class B (MsSPSB and MsSPSB3). While MsSPSA showed nodule-enhanced expression, both MsSPSB genes exhibited leaf-enhanced expression. Alfalfa leaf and nodule SPS enzymes showed differences in chromatographic and electrophoretic migration and differences in V (max) and allosteric regulation. The root nodules in legume plants are a strong sink for photosynthates with its need for ATP, reducing power and carbon skeletons for dinitrogen fixation and ammonia assimilation. The expression of genes encoding SPS and other key enzymes in sucrose metabolism, sucrose phosphate phosphatase and sucrose synthase, was analyzed in the leaves and nodules of plants inoculated with Sinorhizobium meliloti. Based on the expression pattern of these genes, the properties of the SPS isoforms and the concentration of starch and soluble sugars in nodules induced by a wild type and a nitrogen fixation deficient strain, we propose that SPS has an important role in the control of carbon flux into different metabolic pathways in the symbiotic nodules.

  14. GC-MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules.

    Science.gov (United States)

    Barsch, Aiko; Carvalho, Helena G; Cullimore, Julie V; Niehaus, Karsten

    2006-12-15

    In symbiotic interaction with legume plants, bacteria termed Rhizobia can fix massive amounts of atmospheric nitrogen which is primarily provided in the form of ammonium to the host plants. Therefore, legume root nodules that house the symbiotic bacteria are ideally suited to study the process of primary ammonium assimilation. Here, we present a GC-MS based metabolite profiling analysis of Medicago truncatula root nodules (induced by the bacterium Sinorhizobium meliloti) before and after inhibition of glutamine synthetase (GS) by the chemical herbicide phosphinotricine. The primary role of GS in ammonium assimilation was revealed by drastically reduced levels of glutamine in phosphinotricine treated root nodules. In comparison to previous results of increased asparagine synthetase transcript and protein abundances in GS inhibited nodules the metabolic data revealed that decreased amounts of aspartate might preclude taking advantage of this elevated enzymatic activity. A potential role of glutamate dehydrogenase in ammonium assimilation was metabolically indicated 24 and 48 h after GS inhibition. Therefore, nodule ammonium assimilation might in principle involve three interdependent metabolic pathways which are adjusted to control basic nitrogen metabolism.

  15. effect of exogenous application of rhizopine on lucerne root nodulation

    African Journals Online (AJOL)

    BSN

    U1111·ersi1y of Adelaide, South Australia. *Corresspondaning author. AB TRACT. Rhizopine, 3-0 -methyl scyllo-inosamine was applied to the roots of luceme seedling inoculated with either rhizopine synthesizing Sinorhizobium meliloti strain L530 or the non-rhizopine synthesizing strain Rm 1021. There was an initial ...

  16. The DMI1 and DMI2 Early Symbiotic Genes of Medicago truncatula Are Required for a High-Affinity Nodulation Factor-Binding Site Associated to a Particulate Fraction of Roots1

    Science.gov (United States)

    Hogg, Bridget V.; Cullimore, Julie V.; Ranjeva, Raoul; Bono, Jean-Jacques

    2006-01-01

    The establishment of the legume-rhizobia symbiosis between Medicago spp. and Sinorhizobium meliloti is dependent on the production of sulfated lipo-chitooligosaccharidic nodulation (Nod) factors by the bacterial partner. In this article, using a biochemical approach to characterize putative Nod factor receptors in the plant host, we describe a high-affinity binding site (Kd = 0.45 nm) for the major Nod factor produced by S. meliloti. This site is termed Nod factor-binding site 3 (NFBS3). NFBS3 is associated to a high-density fraction prepared from roots of Medicago truncatula and shows binding specificity for lipo-chitooligosaccharidic structures. As for the previously characterized binding sites (NFBS1 and NFBS2), NFBS3 does not recognize the sulfate group on the S. meliloti Nod factor. Studies of Nod factor binding in root extracts of early symbiotic mutants of M. truncatula reveals that the new site is present in Nod factor perception and does not make infections 3 (dmi3) mutants but is absent in dmi1 and dmi2 mutants. Roots and cell cultures of all these mutants still contain sites similar to NFBS1 and NFBS2, respectively. These results suggest that NFBS3 is different from NFBS2 and NFBS1 and is dependent on the common symbiotic genes DMI1 and DMI2 required for establishment of symbioses with both rhizobia and arbuscular mycorrhizal fungi. The potential role of this site in the establishment of root endosymbioses is discussed. PMID:16377749

  17. NADP+ -dependent malic enzyme of Rhizobium meliloti.

    OpenAIRE

    Driscoll, B T; Finan, T M

    1996-01-01

    The bacterium Rhizobium meliloti, which forms N2-fixing root nodules on alfalfa, has two distinct malic enzymes; one is NADP+ dependent, while a second has maximal activity when NAD+ is the coenzyme. The diphosphopyridine nucleotide (NAD+)-dependent malic enzyme (DME) is required for symbiotic N2 fixation, likely as part of a pathway for the conversion of C4-dicarboxylic acids to acetyl coenzyme A in N2-fixing bacteroids. Here, we report the cloning and localization of the tme gene (encoding ...

  18. ORF Sequence: NC_003078 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available etitiveness [Sinorhizobium meliloti 1021] MQLSACARRREAVRYRRRMARILILLFSLLSAFAFPVTPVP... NC_003078 gi|16264863 >gi|16264863|ref|NP_437655.1| probable membrane protein necessary for nodulation comp

  19. Bacterial Molecular Signals in the Sinorhizobium fredii-Soybean Symbiosis

    Directory of Open Access Journals (Sweden)

    Francisco J. López-Baena

    2016-05-01

    Full Text Available Sinorhizobium (Ensifer fredii (S. fredii is a rhizobial species exhibiting a remarkably broad nodulation host-range. Thus, S. fredii is able to effectively nodulate dozens of different legumes, including plants forming determinate nodules, such as the important crops soybean and cowpea, and plants forming indeterminate nodules, such as Glycyrrhiza uralensis and pigeon-pea. This capacity of adaptation to different symbioses makes the study of the molecular signals produced by S. fredii strains of increasing interest since it allows the analysis of their symbiotic role in different types of nodule. In this review, we analyze in depth different S. fredii molecules that act as signals in symbiosis, including nodulation factors, different surface polysaccharides (exopolysaccharides, lipopolysaccharides, cyclic glucans, and K-antigen capsular polysaccharides, and effectors delivered to the interior of the host cells through a symbiotic type 3 secretion system.

  20. Rhizobial strains exert a major effect on the amino acid composition of alfalfa nodules under NaCl stress.

    Science.gov (United States)

    Bertrand, Annick; Bipfubusa, Marie; Dhont, Catherine; Chalifour, François-P; Drouin, Pascal; Beauchamp, Chantal J

    2016-11-01

    Specific amino acids have protective functions in plants under stress conditions. This study assessed the effects of rhizobial strains on the amino acid composition in alfalfa under salt stress. Two alfalfa cultivars (Medicago sativa L. cv Apica and salt-tolerant cv Halo) in association with two Sinorhizobium meliloti strains with contrasting growth under salt stress (strain A2 and salt-tolerant strain Rm1521) were exposed to different levels of NaCl (0, 20, 40, 80 or 160 mM NaCl) under controlled conditions. We compared root and shoot biomasses, as well as root:shoot ratio for each association under these conditions as indicators of the salt tolerance of the symbiosis. Amino acid concentrations were analyzed in nodules, leaves and roots. The total concentration of free amino acids in nodules was mostly rhizobial-strain dependent while in leaves and roots it was mostly responsive to salt stress. For both cultivars, total and individual concentrations of amino acids including asparagine, proline, glutamine, aspartate, glutamate, γ-aminobutyric acid (GABA), histidine and ornithine were higher in Rm1521 nodules than in A2 nodules. Conversely, lysine and methionine were more abundant in A2 nodules than in Rm1521 nodules. Proline, glutamine, arginine, GABA and histidine substantially accumulated in salt-stressed nodules, suggesting an enhanced production of amino acids associated with osmoregulation, N storage or energy metabolism to counteract salt stress. Combining the salt-tolerant strain Rm1521 and the salt-tolerant cultivar Halo enhanced the root:shoot ratios and amino acid concentrations involved in plant protection which could be in part responsible for the enhancement of salt tolerance in alfalfa. Crown Copyright © 2016. Published by Elsevier Masson SAS. All rights reserved.

  1. Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya.

    Science.gov (United States)

    Nick, G; de Lajudie, P; Eardly, B D; Suomalainen, S; Paulin, L; Zhang, X; Gillis, M; Lindström, K

    1999-10-01

    SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of Acacia senegal and Prosopis chilensis. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridization, genomic fingerprinting using repetitive sequence-based PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus Sinorhizobium. Two of the strains grouped with Sinorhizobium saheli and seven with Sinorhizobium terangae, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species, Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov.

  2. Expression of nodule-specific genes in alfalfa root nodules blocked at an early stage of development.

    NARCIS (Netherlands)

    Dickstein, R.; Bisseling, T.; Reinhold, V.N.; Ausubel, F.M.

    1988-01-01

    To help dissect the molecular basis of the Rhizobium-legume symbiosis, we used in vitro translation and Northern blot analysis of nodule RNA to examine alfalfa-specific genes (nodulins) expressed in two types of developmentally defective root nodules elicited by Rhizobium meliloti. Fix- nodules were

  3. Nodulin gene expression and ENOD2 localization in effective, nitrogen fixing and ineffective, bacteria-free nodules of alfalfa.

    NARCIS (Netherlands)

    Wiel, van de C.C.M.; Nurris, J.H.; Bocheneck, B.; Dickstein, R.; Bisseling, T.; Hirsch, A.M.

    1990-01-01

    Alfalfa plants form bacteria-free nodules in response to a number of agents, including Rhizobium meliloti exo mutants, Agrobacterium tumefaciens transconjugants carrying cloned R. meliloti nodulation genes, and compounds that function as auxin transport inhibitors, N-( 1-naphthyl)phthalamic acid or

  4. An ABC-Type Cobalt Transport System Is Essential for Growth of Sinorhizobium melilotiat Trace Metal Concentrations ▿ †

    Science.gov (United States)

    Cheng, Jiujun; Poduska, Branislava; Morton, Richard A.; Finan, Turlough M.

    2011-01-01

    We report expression and mutant phenotypes for a gene cluster in Sinorhizobium meliloti, designated cbtJKL, that has been shown to encode an ABC-type cobalt transport system. Transcription of cbtJKLinitiated 384 nucleotides upstream from the cbtJtranslation start codon, and the resulting 5′ region contained a putative B12riboswitch. Expression of the cbtJKLgenes appeared to be controlled by (cobalt-loaded) cobalamin interacting at the B12riboswitch, since (i) a putative B12riboswitch was located within this large upstream region, (ii) cbtJtranscription was repressed upon addition of cobalt or vitamin B12, and (iii) deletions in the B12riboswitch resulted in constitutive cbtJKLtranscription. Insertion mutants in cbtJKLfailed to grow in LB medium, and growth was restored through the addition of cobalt but not other metals. This growth phenotype appeared to be due to the chelation of cobalt present in LB, and cbtJKLmutants also failed to grow in minimal medium containing the chelating agent EDTA unless the medium was supplemented with additional or excess cobalt. In uptake experiments, 57Co2+accumulation was high in wild-type cells expressing the cbtJKLgenes, whereas wild-type cells in which cbtJKLexpression was repressed showed reduced accumulation. In cbtJKLmutant cells, 57Co2+accumulation was reduced relative to that of the wild type, and presumably, this residual cobalt transport occurred via an alternate ion uptake system(s) that is not specific to cobalt. In symbiosis, the alternate system(s) appeared to mediate cobalt transport into bacteroid cells, as low cbtJKLexpression was detected in bacteroids and cbtJKLmutants formed N2-fixing nodules on alfalfa. PMID:21725018

  5. The Rhizobium meliloti putA gene: its role in the establishment of the symbiotic interaction with alfalfa.

    Science.gov (United States)

    Jiménez-Zurdo, J I; García-Rodríguez, F M; Toro, N

    1997-01-01

    Little is known about the energy sources used by rhizobia during colonization, invasion and root nodule formation on leguminous plants. We have recently reported that an impaired proline metabolism in rhizobium meliloti leads to a reduced nodulation efficiency and competitiveness on alfalfa roots. In the present study we have characterized the R. meliloti proline dehydrogenase gene (putA) and addressed the question of its role in symbiosis. This rhizobial gene encodes a 1224-amino-acid-long polypeptide which is homologous to enteric bacteria, Rhodobacter capsulatus and Bradyrhizobium japonicum PutA proteins. Like the situation in these bacteria, sequence analysis identified the proline dehydrogenase (PDH) and pyrroline-5-carboxylate dehydrogenase (P5CDH) domains in the R. meliloti putA-encoded protein. Beta-galactosidase assays performed with free-living cells carrying a putA-lacZ transcriptional fusion revealed that R. meliloti putA gene expression is induced by proline, autoregulated by its encoded product, and independent of the general nitrogen regulatory system (Ntr). In addition, analysis of putA expression during the different steps of the symbiotic interaction with alfalfa showed that expression of this gene is turned on by the root exudates (RE), during root invasion and nodule formation, but not in differentiated nitrogen-fixing bacteroids. Furthermore, we show that the PutA- phenotype leads to a significant reduction of alfalfa root colonization by R. meliloti.

  6. Rhizobium meliloti mutants that overproduce the R. meliloti acidic Calcofluor-binding exopolysaccharide

    International Nuclear Information System (INIS)

    Doherty, D.; Glazebrook, J.; Walker, G.C.; Leigh, J.A.

    1988-01-01

    The acidic Calcofluor-binding exopolysaccharide of Rhizobium meliloti Rm1021 plays one or more critical roles in nodule invasion and possible in nodule development. Two loci, exoR and exoS, that effect the regulation of synthesis of this exopolysaccharide were identified by screening for derivatives of strain Rm1021 that formed mucoid colonies that fluoresced extremely brightly under UV light when grown on medium containing Calcofluor. The exopolysaccharide produced in large quantities by the exoR95::Tn5 and exoS96::Tn5 strains was indistinguishable from that produced by the parental strain Rm1021, and its synthesis required the function of at least the exoA, exoB, and exoF genes. Both the exoR and exoS loci were located on the chromosome, and the exo96::Tn5 mutation was 84% linked to the trp-33 mutation by ΦM12 transduction. Synthesis of the Calcofluor-binding exopolysaccharide by strain Rm1021 was greatly stimulated by starvation for ammonia. In contrast, the exoR95::Tn5 mutant produced high levels of exopolysaccharide regardless of the presence or absence of ammonia in the medium. The exoS96::Tn5 mutant produced elevated amounts of exopolysaccharide in the presence of ammonia, but higher amounts were observed after starvation for ammonia. The presence of either mutation increased the level of expression of exoF::TnphoA and exoP::TnphoA fusions. Analyses of results obtained when alfalfa seedlings were inoculated with the exoR95::Tn5 strain indicated that the mutant strain could not invade nodules. However, pseudorevertants that retained the original exoR95::Tn5 mutant but acquired unlinked suppressors so that they produced an approximately normal amount of exopolysaccharide were able to invade nodules and fix nitrogen

  7. Toxic effects of arsenic on Sinorhizobium-Medicago sativa symbiotic interaction.

    Science.gov (United States)

    Pajuelo, Eloísa; Rodríguez-Llorente, Ignacio D; Dary, Mohammed; Palomares, Antonio J

    2008-07-01

    Recently, the Rhizobium-legume symbiotic interaction has been proposed as an interesting tool in bioremediation. However, little is known about the effect of most common contaminants on this process. The phytotoxic effects of arsenic on nodulation of Medicago sativa have been examined in vitro using the highly arsenic resistant and symbiotically effective Sinorhizobium sp. strain MA11. The bacteria were able to grow on plates containing As concentrations as high as 10 mM. Nevertheless, as little as 25-35 microM arsenite produced a 75% decrease in the total number of nodules, due to a 90% reduction in the number of rhizobial infections, as could be determined using the strain MA11 carrying a lacZ reporter gene. This effect was associated to root hair damage and a shorter infective root zone. However, once nodulation was established nodule development seemed to continue normally, although earlier senescence could be observed in nodules of arsenic-grown plants.

  8. Flavonoids Released Naturally from Alfalfa Seeds Enhance Growth Rate of Rhizobium meliloti1

    Science.gov (United States)

    Hartwig, Ueli A.; Joseph, Cecillia M.; Phillips, Donald A.

    1991-01-01

    Alfalfa (Medicago sativa L.) releases different flavonoids from seeds and roots. Imbibing seeds discharge 3′,4′,5,7-substituted flavonoids; roots exude 5-deoxy molecules. Many, but not all, of these flavonoids induce nodulation (nod) genes in Rhizobium meliloti. The dominant flavonoid released from alfalfa seeds is identified here as quercetin-3-O-galactoside, a molecule that does not induce nod genes. Low concentrations (1-10 micromolar) of this compound, as well as luteolin-7-O-glucoside, another major flavonoid released from germinating seeds, and the aglycones, quercetin and luteolin, increase growth rate of R. meliloti in a defined minimal medium. Tests show that the 5,7-dihydroxyl substitution pattern on those molecules was primarily responsible for the growth effect, thus explaining how 5-deoxy flavonoids in root exudates fail to enhance growth of R. meliloti. Luteolin increases growth by a mechanism separate from its capacity to induce rhizobial nod genes, because it still enhanced growth rate of R. meliloti lacking functional copies of the three known nodD genes. Quercetin and luteolin also increased growth rate of Pseudomonas putida. They had no effect on growth rate of Bacillus subtilis or Agrobacterium tumefaciens, but they slowed growth of two fungal pathogens of alfalfa. These results suggest that alfalfa can create ecochemical zones for controlling soil microbes by releasing structurally different flavonoids from seeds and roots. PMID:16668056

  9. Two Plant Bacteria, S. meliloti and Ca. Liberibacter asiaticus, Share Functional znuABC Homologues That Encode for a High Affinity Zinc Uptake System

    OpenAIRE

    Vahling-Armstrong, Cheryl M.; Zhou, Huasong; Benyon, Lesley; Morgan, J. Kent; Duan, Yongping

    2012-01-01

    The Znu system, encoded for by znuABC, can be found in multiple genera of bacteria and has been shown to be responsible for the import of zinc under low zinc conditions. Although this high-affinity uptake system is known to be important for both growth and/or pathogenesis in bacteria, it has not been functionally characterized in a plant-associated bacterium. A single homologue of this system has been identified in the plant endosymbiont, Sinorhizobium meliloti, while two homologous systems w...

  10. Structure and Biological Roles of Sinorhizobium fredii HH103 Exopolysaccharide

    Science.gov (United States)

    Acosta-Jurado, Sebastián; Soto, María J.; Margaret, Isabel; Crespo-Rivas, Juan C.; Sanjuan, Juan; Temprano, Francisco; Gil-Serrano, Antonio; Ruiz-Sainz, José E.; Vinardell, José M.

    2014-01-01

    Here we report that the structure of the Sinorhizobium fredii HH103 exopolysaccharide (EPS) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. A S. fredii HH103 exoA mutant (SVQ530), unable to produce EPS, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. Mutant SVQ530 is, however, less competitive to nodulate Vigna unguiculata. Biofilm formation was reduced in mutant SVQ530 but increased in an EPS overproducing mutant. Mutant SVQ530 was impaired in surface motility and showed higher osmosensitivity compared to its wild type strain in media containing 50 mM NaCl or 5% (w/v) sucrose. Neither S. fredii HH103 nor 41 other S. fredii strains were recognized by soybean lectin (SBL). S. fredii HH103 mutants affected in exopolysaccharides (EPS), lipopolysaccharides (LPS), cyclic glucans (CG) or capsular polysaccharides (KPS) were not significantly impaired in their soybean-root attachment capacity, suggesting that these surface polysaccharides might not be relevant in early attachment to soybean roots. These results also indicate that the molecular mechanisms involved in S. fredii attachment to soybean roots might be different to those operating in Bradyrhizobium japonicum. PMID:25521500

  11. Toxic effects of arsenic on Sinorhizobium-Medicago sativa symbiotic interaction

    Energy Technology Data Exchange (ETDEWEB)

    Pajuelo, Eloisa [Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville (Spain); Rodriguez-Llorente, Ignacio D. [Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville (Spain)], E-mail: irodri@us.es; Dary, Mohammed; Palomares, Antonio J. [Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville (Spain)

    2008-07-15

    Recently, the Rhizobium-legume symbiotic interaction has been proposed as an interesting tool in bioremediation. However, little is known about the effect of most common contaminants on this process. The phytotoxic effects of arsenic on nodulation of Medicago sativa have been examined in vitro using the highly arsenic resistant and symbiotically effective Sinorhizobium sp. strain MA11. The bacteria were able to grow on plates containing As concentrations as high as 10 mM. Nevertheless, as little as 25-35 {mu}M arsenite produced a 75% decrease in the total number of nodules, due to a 90% reduction in the number of rhizobial infections, as could be determined using the strain MA11 carrying a lacZ reporter gene. This effect was associated to root hair damage and a shorter infective root zone. However, once nodulation was established nodule development seemed to continue normally, although earlier senescence could be observed in nodules of arsenic-grown plants. - First steps of nodulation of alfalfa, in particular infection thread formation, are more sensitive to As than nitrogen fixation due to plant effects.

  12. Infection and Invasion of Roots by Symbiotic, Nitrogen-Fixing Rhizobia during Nodulation of Temperate Legumes

    OpenAIRE

    Gage, Daniel J.

    2004-01-01

    Bacteria belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. The interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. Temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that a...

  13. Thyroid Nodules

    Science.gov (United States)

    Thyroid nodules Overview Thyroid nodules are solid or fluid-filled lumps that form within your thyroid, a small gland located at the base of ... just above your breastbone. The great majority of thyroid nodules aren't serious and don't cause ...

  14. Manganese nodules

    Science.gov (United States)

    Hein, James R.; Harff, Jan; Petersen, Sven; Thiede, Jorn

    2016-01-01

    The existence of manganese (Mn) nodules (Figure 1) has been known since the late 1800s when they were collected during the Challenger expedition of 1873–1876. However, it was not until after WWII that nodules were further studied in detail for their ability to adsorb metals from seawater. Many of the early studies did not distinguish Mn nodules from Mn crusts. Economic interest in Mn nodules began in the late 1950s and early 1960s when John Mero finished his Ph.D. thesis on this subject, which was published in the journal Economic Geology (Mero, 1962) and later as a book (Mero, 1965). By the mid-1970s, large consortia had formed to search for and mine Mn nodules that occur between the Clarion and Clipperton fracture zones (CCZ) in the NE Pacific (Figure 2). This is still the area considered of greatest economic potential in the global ocean because of high nickel (Ni), copper (Cu), and Mn contents and the dense distribution of nodules in the area. While the mining of nodules was fully expected to begin in the late 1970s or early 1980s, this never occurred due to a downturn in the price of metals on the global market. Since then, many research cruises have been undertaken to study the CCZ nodules, and now 15 contracts for exploration sites have been given or are pending by the International Seabed Authority (ISA). Many books and science journal articles have been published summarizing the early work (e.g., Baturin, 1988; Halbach et al., 1988), and research has continued to the present day (e.g., ISA, 1999; ISA, 2010). Although the initial attraction for nodules was their high Ni, Cu, and Mn contents, subsequent work has shown that nodules host large quantities of other critical metals needed for high-tech, green-tech, and energy applications (Hein et al., 2013; Hein and Koschinsky, 2014).

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

    Directory of Open Access Journals (Sweden)

    Nieto Joaquín J

    2010-07-01

    Full Text Available Abstract 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

  16. Thyroid nodule

    Science.gov (United States)

    ... symptoms, including: Fatigue Palpitations Chest pain Memory loss Thyroid nodules are sometimes found in people who have Hashimoto's disease. This may cause symptoms of an underactive thyroid gland, such as: Dry ...

  17. Solitary pulmonary nodule

    Science.gov (United States)

    Lung cancer - solitary nodule; Infectious granuloma - pulmonary nodule; SPN ... More than half of all solitary pulmonary nodules are noncancerous ... infections. Infectious granulomas (which are formed by cells as ...

  18. Chrysoeriol and Luteolin Released from Alfalfa Seeds Induce nod Genes in Rhizobium meliloti1

    Science.gov (United States)

    Hartwig, Ueli A.; Maxwell, Carl A.; Joseph, Cecillia M.; Phillips, Donald A.

    1990-01-01

    Flavonoid signals from alfalfa (Medicago sativa L.) seed and root exudates induce transcription of nodulation (nod) genes in Rhizobium meliloti. The flavone luteolin previously was isolated from alfalfa seeds by other workers and identified as the first nod gene inducer for R. meliloti. Our recent study of `Moapa 69' alfalfa root exudates found no luteolin but did identify three other nod gene inducers: 4,4′-dihydroxy-2′-methoxychalcone, 4′,7-dihydroxyflavone, and 4′,7-dihydroxyflavanone. The goal of the current study was to identify and quantify nod gene-inducing flavonoids that may influence Rhizobium populations around a germinating alfalfa seed. Aqueous rinses of Moapa 69 alfalfa seeds were collected and assayed for induction of a nodABC-lacZ fusion in R. meliloti. During the first 4 hours of imbibition, total nod gene-inducing activity was released from seeds at 100-fold higher rates than from roots of 72-hour-old seedlings. Five flavonoids were purified and identified by spectroscopic analyses (ultraviolet/visible absorbance, proton nuclear magnetic resonance, and mass spectroscopy) and comparison with authentic standards. Two very active nod gene-inducing flavonoids, chrysoeriol (3′-methoxyluteolin) and luteolin, were identified in seed rinses. Luteolin required a higher concentration (18 nanomolar) than chrysoeriol (5 nanomolar) for half-maximum induction of nodABC-lacZ in R. meliloti, and both were less active than 4,4′-dihydroxy-2′-methoxychalcone (2 nanomolar) from root exudates. Seeds exuded three other luteolin derivatives: luteolin-7-O-glucoside, 5-methoxyluteolin, and 3′,5-dimethoxyluteolin. Their combined quantities were 24-fold greater than that of luteolin plus chrysoeriol. Most nod gene-inducing activity of these luteolin derivatives apparently is associated with degradation to luteolin and chrysoeriol. However, their presence in large quantities suggests that they may contribute significantly to nod gene-inducing activity in the

  19. A Transposable Partitioning Locus Used To Stabilize Plasmid-Borne Hydrogen Oxidation and Trifolitoxin Production Genes in a Sinorhizobium Strain

    Science.gov (United States)

    Kent, Angela D.; Wojtasiak, Michelle L.; Robleto, Eduardo A.; Triplett, Eric W.

    1998-01-01

    Improved nitrogen-fixing inoculum strains for leguminous crops must be able to effectively compete with indigenous strains for nodulation, enhance legume productivity compared to the productivity obtained with indigenous strains, and maintain stable expression of any added genes in the absence of selection pressure. We constructed a transposable element containing the tfx region for expression of increased nodulation competitiveness and the par locus for plasmid stability. The transposon was inserted into tetA of pHU52, a broad-host-range plasmid conferring the H2 uptake phenotype. The resulting plasmid, pHUTFXPAR, conferred the plasmid stability, trifolitoxin production, and H2 uptake phenotypes in the broad-host-range organism Sinorhizobium sp. strain ANU280. The broad applications of a transposon conferring plasmid stability are discussed. PMID:9572932

  20. The RpiR-Like Repressor IolR Regulates Inositol Catabolism in Sinorhizobium meliloti▿†

    Science.gov (United States)

    Kohler, Petra R. A.; Choong, Ee-Leng; Rossbach, Silvia

    2011-01-01

    Sinorhizobium meliloti, the nitrogen-fixing symbiont of alfalfa, has the ability to catabolize myo-, scyllo-, and d-chiro-inositol. Functional inositol catabolism (iol) genes are required for growth on these inositol isomers, and they play a role during plant-bacterium interactions. The inositol catabolism genes comprise the chromosomally encoded iolA (mmsA) and the iolY(smc01163)RCDEB genes, as well as the idhA gene located on the pSymB plasmid. Reverse transcriptase assays showed that the iolYRCDEB genes are transcribed as one operon. The iol genes were weakly expressed without induction, but their expression was strongly induced by myo-inositol. The putative transcriptional regulator of the iol genes, IolR, belongs to the RpiR-like repressor family. Electrophoretic mobility shift assays demonstrated that IolR recognized a conserved palindromic sequence (5′-GGAA-N6-TTCC-3′) in the upstream regions of the idhA, iolY, iolR, and iolC genes. Complementation assays found IolR to be required for the repression of its own gene and for the downregulation of the idhA-encoded myo-inositol dehydrogenase activity in the presence and absence of inositol. Further expression studies indicated that the late pathway intermediate 2-keto-5-deoxy-d-gluconic acid 6-phosphate (KDGP) functions as the true inducer of the iol genes. The iolA (mmsA) gene encoding methylmalonate semialdehyde dehydrogenase was not regulated by IolR. The S. meliloti iolA (mmsA) gene product seems to be involved in more than only the inositol catabolic pathway, since it was also found to be essential for valine catabolism, supporting its more recent annotation as mmsA. PMID:21784930

  1. Two-component regulatory system ActS/ActR is required for Sinorhizobium meliloti adaptation to oxidative stress.

    Science.gov (United States)

    Tang, Guirong; Wang, Sunjun; Lu, Dawei; Huang, Leqi; Li, Ningning; Luo, Li

    2017-05-01

    The two-component system ActS/ActR plays important roles in bacterial adaptation to abiotic stress, including acid tolerance and oxidant resistance. However, the underlying regulatory mechanism is not clear. In this study, we found that the ActS/ActR system is required for adaptation to oxidative stress by regulating the transcription of the genes actR, katB, gshA and gshB1. The actS and actR mutants were sensitive to low pH and oxidants such as H 2 O 2 , oxidized glutathione (GSSG) and sodium nitroprusside (SNP). The expression of actR by using a plasmid rescued the defect of SNP sensitivity for all actS and actR mutants. The expression of actS and actR were suppressed by treatment with H 2 O 2 . The expression of actS, actR, oxyR, katA and katB was required for ActS and ActR under normal conditions. The induction of katB, gshA and gshB1 depended on ActS and ActR during treatment with H 2 O 2 and SNP. Our findings revealed that the ActS/ActR system is a key redox regulator in S. meliltoi and provides a new cue to understanding Rhizobium-legume symbiosis. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  2. A FIELD STUDY WITH GENETICALLY ENGINEERED ALFALFA INOCULATED WITH RECOMBINANT SINORHIZOBIUM MELILOTI: EFFECTS ON THE SOIL ECOSYSTEM

    Science.gov (United States)

    The agricultural use of genetically engineered plants and microorganisms has become increasingly common. Because genetically engineered plants and microorganisms can produce compounds foreign to their environment, there is concern that they may become established outside of thei...

  3. Polychlorinated biphenyl rhizoremediation by Pseudomonas fluorescens F113 derivatives, using a Sinorhizobium meliloti nod system to drive bph gene expression

    Czech Academy of Sciences Publication Activity Database

    Villacieros, M.; Whelan, C.; Macková, Martina; Molgaard, J.; Sánchez-Contreras, M.; Lloret, J.; Cárcer de, D.; Oruezábal, R. I.; Bolanos, L.; Macek, Tomáš; Karlson, U.; Dowling, D. N.; Martín, M.; Rivilla, R.

    2005-01-01

    Roč. 71, č. 5 (2005), 2687-2694 ISSN 0099-2240 Grant - others:5thFW(XE) QLK3-CT-2001-00101; European Commission(XE) BIO4-CT97-2227 Institutional research plan: CEZ:AV0Z4055905 Keywords : polychlorinated biphenyls * rhizoremediation Subject RIV: CC - Organic Chemistry Impact factor: 3.818, year: 2005

  4. Root and Nodulation Phenotypes of the Ethylene-Insensitive Sickle Mutant of Medicago truncatula

    Directory of Open Access Journals (Sweden)

    JOKO PRAYITNO

    2010-09-01

    Full Text Available The sickle (skl mutant of the model legume Medicago truncatula is an ethylene-sensitive mutant that have a ten-fold increase in nodule numbers. The nodulation and root phenotypes of the skl mutant were investigated and further characterised. The skl mutant had longer roots than the wild type, but when inoculated with Sinorhizobium, its root length was reduced to the level of wild type. Furthermore, lateral root numbers in uninoculated skl were similar to those in uninoculated wild type. However, when the root tips were decapitated, fewer lateral roots formed in skl than in wild type. Nodule numbers of the skl mutant were significantly reduced by low nitrate concentration (2.5 mM. These results suggest that skl mutant has alterations in both root and nodule development.

  5. The nitrate-reduction gene cluster components exert lineage-dependent contributions to optimization of Sinorhizobium symbiosis with soybeans.

    Science.gov (United States)

    Liu, Li Xue; Li, Qin Qin; Zhang, Yun Zeng; Hu, Yue; Jiao, Jian; Guo, Hui Juan; Zhang, Xing Xing; Zhang, Biliang; Chen, Wen Xin; Tian, Chang Fu

    2017-12-01

    Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate-reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S. sp. III. In S. fredii, the deletion mutation of the nap (nitrate reductase), instead of nir (nitrite reductase) and nor (nitric oxide reductase), led to defects in nitrogen-fixation (Fix - ). By contrast, none of these core nitrate-reduction genes were required for the symbiosis of S. sp. III. However, within the same gene cluster, the deletion of hemN1 (encoding oxygen-independent coproporphyrinogen III oxidase) in both S. fredii and S. sp. III led to the formation of nitrogen-fixing (Fix + ) but ineffective (Eff - ) nodules. These Fix + /Eff - nodules were characterized by significantly lower enzyme activity of glutamine synthetase indicating rhizobial modulation of nitrogen-assimilation by plants. A distant homologue of HemN1 from S. sojae can complement this defect in S. fredii and S. sp. III, but exhibited a more pleotropic role in symbiosis establishment. These findings highlighted the lineage-dependent optimization of symbiotic functions in different rhizobial species associated with the same host. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Rhizobium NodB protein involved in nodulation signal synthesis is a chitooligosaccharide deacetylase.

    Science.gov (United States)

    John, M; Röhrig, H; Schmidt, J; Wieneke, U; Schell, J

    1993-01-15

    The common nodulation genes nodABC are conserved in all rhizobia and are involved in synthesis of a lipooligosaccharide signal molecule. This bacterial signal consists of a chitooligosaccharide backbone, which carries at the nonreducing end a fatty acyl chain. The modified chitooligosaccharide molecule triggers development of nodules on the roots of the leguminous host plant. To elucidate the specific role of the NodB protein in nodulation factor synthesis, we have purified recombinant NodB and determined its biochemical role by direct assays. Our data show that the NodB protein of Rhizobium meliloti deacetylates the nonreducing N-acetylglucosamine residue of chitooligosaccharides. The monosaccharide N-acetylglucosamine is not deacetylated by NodB. In the pathway of Nod factor synthesis, deacetylation at the nonreducing end of the oligosaccharide backbone may be a necessary requirement for attachment of the fatty acyl chain.

  7. Identification of Sinorhizobium (Ensifer) medicae based on a specific genomic sequence unveiled by M13-PCR fingerprinting.

    Science.gov (United States)

    Dourado, Ana Catarina; Alves, Paula I L; Tenreiro, Tania; Ferreira, Eugénio M; Tenreiro, Rogério; Fareleira, Paula; Crespo, M Teresa Barreto

    2009-12-01

    A collection of nodule isolates from Medicago polymorpha obtained from southern and central Portugal was evaluated by M13-PCR fingerprinting and hierarchical cluster analysis. Several genomic clusters were obtained which, by 16S rRNA gene sequencing of selected representatives, were shown to be associated with particular taxonomic groups of rhizobia and other soil bacteria. The method provided a clear separation between rhizobia and co-isolated non-symbiotic soil contaminants. Ten M13-PCR groups were assigned to Sinorhizobium (Ensifer) medicae and included all isolates responsible for the formation of nitrogen-fixing nodules upon re-inoculation of M. polymorpha test-plants. In addition, enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting indicated a high genomic heterogeneity within the major M13- PCR clusters of S. medicae isolates. Based on nucleotide sequence data of an M13-PCR amplicon of ca. 1500 bp, observed only in S. medicae isolates and spanning locus Smed_3707 to Smed_3709 from the pSMED01 plasmid sequence of S. medicae WSM419 genome's sequence, a pair of PCR primers was designed and used for direct PCR amplification of a 1399-bp sequence within this fragment. Additional in silico and in vitro experiments, as well as phylogenetic analysis, confirmed the specificity of this primer combination and therefore the reliability of this approach in the prompt identification of S. medicae isolates and their distinction from other soil bacteria.

  8. Biogeography of a Novel Ensifer meliloti Clade Associated with the Australian Legume Trigonella suavissima.

    Science.gov (United States)

    Eardly, Bertrand; Elia, Patrick; Brockwell, John; Golemboski, Daniel; van Berkum, Peter

    2017-05-15

    Here, we describe a novel clade within Ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, Medicago L., Melilotus Mill., and Trigonella L., which are members of the tribe Trifolieae. These legumes have a natural distribution extending from the Mediterranean Basin through western Asia, where there is an unsurpassed number of species belonging to these genera. Trigonella suavissima L. is unusual in that it is the only species in the tribe Trifolieae that is native to Australia. We compared the genetic diversity and taxonomic placement of rhizobia nodulating T. suavissima with those of members of an Ensifer reference collection. Our goal was to determine if the T. suavissima rhizobial strains, like their plant host, are naturally limited to the Australian continent. We used multilocus sequence analysis to estimate the genetic relatedness of 56 T. suavissima symbionts to 28 Ensifer reference strains. Sequence data were partitioned according to the replicons in which the loci are located. The results were used to construct replicon-specific phylogenetic trees. In both the chromosomal and chromid trees, the Australian strains formed a distinct clade within E. meliloti The strains also shared few alleles with Ensifer reference strains from other continents. Carbon source utilization assays revealed that the strains are also unusual in their ability to utilize 2-oxoglutarate as a sole carbon source. A strategy was outlined for locating similar strains elsewhere. IMPORTANCE In this study, we employed a biogeographical approach to investigate the origins of a symbiotic relationship between an Australian legume and its nitrogen-fixing rhizobia. The question of the ancestral origins of these symbionts is based on the observation that the legume host is not closely

  9. Sinorhizobium fredii USDA257 Translocates NopP into Vigna unguiculata Root Nodules

    Science.gov (United States)

    Type III secretion systems (T3SSs), which are found in many Gram-negative bacterial pathogens, inject virulence proteins directly into host cells during infection. T3SSs are also present in some strains of rhizobia, bacteria that form symbiotic associations with legumes and fix nitrogen in speciali...

  10. Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America.

    Science.gov (United States)

    Haukka, K; Lindström, K; Young, J P

    1998-02-01

    The diversity and phylogeny of nodA and nifH genes were studied by using 52 rhizobial isolates from Acacia senegal, Prosopis chilensis, and related leguminous trees growing in Africa and Latin America. All of the strains had similar host ranges and belonged to the genera Sinorhizobium and Mesorhizobium, as previously determined by 16S rRNA gene sequence analysis. The restriction patterns and a sequence analysis of the nodA and nifH genes divided the strains into the following three distinct groups: sinorhizobia from Africa, sinorhizobia from Latin America, and mesorhizobia from both regions. In a phylogenetic tree also containing previously published sequences, the nodA genes of our rhizobia formed a branch of their own, but within the branch no correlation between symbiotic genes and host trees was apparent. Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries. Most strains had plasmids, and the presence of plasmid-borne nifH was demonstrated by hybridization for some examples. The nodA and nifH genes of Sinorhizobium teranga ORS1009T grouped with the nodA and nifH genes of the other African sinorhizobia, but Sinorhizobium saheli ORS609T had a totally different nodA sequence, although it was closely related based on the 16S rRNA gene and nifH data. This might be because this S. saheli strain was originally isolated from Sesbania sp., which belongs to a different cross-nodulation group than Acacia and Prosopis spp. The factors that appear to have influenced the evolution of rhizobial symbiotic genes vary in importance at different taxonomic levels.

  11. Three Phylogenetic Groups of nodA and nifH Genes in Sinorhizobium and Mesorhizobium Isolates from Leguminous Trees Growing in Africa and Latin America

    Science.gov (United States)

    Haukka, Kaisa; Lindström, Kristina; Young, J. Peter W.

    1998-01-01

    The diversity and phylogeny of nodA and nifH genes were studied by using 52 rhizobial isolates from Acacia senegal, Prosopis chilensis, and related leguminous trees growing in Africa and Latin America. All of the strains had similar host ranges and belonged to the genera Sinorhizobium and Mesorhizobium, as previously determined by 16S rRNA gene sequence analysis. The restriction patterns and a sequence analysis of the nodA and nifH genes divided the strains into the following three distinct groups: sinorhizobia from Africa, sinorhizobia from Latin America, and mesorhizobia from both regions. In a phylogenetic tree also containing previously published sequences, the nodA genes of our rhizobia formed a branch of their own, but within the branch no correlation between symbiotic genes and host trees was apparent. Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries. Most strains had plasmids, and the presence of plasmid-borne nifH was demonstrated by hybridization for some examples. The nodA and nifH genes of Sinorhizobium teranga ORS1009T grouped with the nodA and nifH genes of the other African sinorhizobia, but Sinorhizobium saheli ORS609T had a totally different nodA sequence, although it was closely related based on the 16S rRNA gene and nifH data. This might be because this S. saheli strain was originally isolated from Sesbania sp., which belongs to a different cross-nodulation group than Acacia and Prosopis spp. The factors that appear to have influenced the evolution of rhizobial symbiotic genes vary in importance at different taxonomic levels. PMID:9464375

  12. Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

    Directory of Open Access Journals (Sweden)

    Przemyslaw Decewicz

    2017-06-01

    Full Text Available The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes. In addition to the previously identified temperate phage, ΦLM21, and the phage-plasmid, pLM21S1, the analysis revealed the presence of three prophage regions. Moreover, four novel phage-encoded DNA methyltransferase (MTase genes were identified and the enzymes were characterized. It was shown that two of the identified viral MTases methylated the same target sequence (GANTC as cell cycle-regulated methyltransferase (CcrM of the bacterial host strain, LM21. This discovery was recognized as an example of the evolutionary convergence between enzymes of sinorhizobial viruses and their host, which may play an important role in virus cycle. In the last part of the study, thorough comparative analyses of 31 sinorhizobial (prophages (including active sinorhizobial phages and novel putative prophages retrieved and manually re-annotated from Sinorhizobium spp. genomes were performed. The networking analysis revealed the presence of highly conserved proteins (e.g., holins and endolysins and a high diversity of viral integrases. The analysis also revealed a large number of viral DNA MTases, whose genes were frequently located within the predicted replication modules of analyzed prophages, which may suggest their important regulatory role. Summarizing, complex analysis of the phage protein similarity network enabled a new insight into overall sinorhizobial virome diversity.

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

    Science.gov (United States)

    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.

  14. Final report for DOE grant FG02-06ER15805

    Energy Technology Data Exchange (ETDEWEB)

    Gage, Daniel

    2012-05-31

    DOE funding was used to investigate the role of the phosphotransferase system (PTS) in the symbiotic, nodulating bacterium Sinorhizobium meliloti. This system is well studied in several bacterial species. However, it's organization and function in S. meliloti is substantially different than in the those other, well-studied bacteria. The S. meliloti PTS, through our DOE-funded work, has become a model for how this important signal transduction system works in the a-proteobacteria. We have found that the PTS is relatively simple, used for only signal transduction and not transport, and is involved in regulation of carbon metabolism in response to carbon availability and nitrogen availability.

  15. Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria.

    Science.gov (United States)

    Martínez-Hidalgo, Pilar; Galindo-Villardón, Purificación; Trujillo, Martha E; Igual, José M; Martínez-Molina, Eustoquio

    2014-09-17

    Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed.

  16. Management of Pulmonary Nodules

    OpenAIRE

    Arvin Aryan

    2010-01-01

    Pulmonary nodule characterization is currently being redefined as new clinical, radiological and pathological data are reported, necessitating a reevaluation of the clinical management."nIn approach to an incidentally detected pulmonary nodule, we should consider that there are different risk situations, different lesion morphologies, and different sizes with various management options."nIn this session we will review the different risk situations for patients with pulmonary nodules...

  17. Micromonospora is a normal occupant of actinorhizal nodules

    Indian Academy of Sciences (India)

    Supplementary table 1. Number of isolates per nodule. Nodule Colonies Average Nodule Colonies Average. AV1 Nodule 1 2 13 EEM Nodule 1 17 9.4. Nodule 2 O Nodule 2 13. Nodule 3 2 Nodule 3 9. AV2 Nodule 1 19 16.1 Nodule 4 7. Nodule 2 25 Nodule 5 18. Nodule 3 38 Nodule 6 4. AV4 Nodule 1 8 14.0 Nodule 7 12.

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

    Science.gov (United States)

    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.

  19. The symbiotic biofilm of Sinorhizobium fredii SMH12, necessary for successful colonization and symbiosis of Glycine max cv Osumi, is regulated by Quorum Sensing systems and inducing flavonoids via NodD1.

    Directory of Open Access Journals (Sweden)

    Francisco Pérez-Montaño

    Full Text Available Bacterial surface components, especially exopolysaccharides, in combination with bacterial Quorum Sensing signals are crucial for the formation of biofilms in most species studied so far. Biofilm formation allows soil bacteria to colonize their surrounding habitat and survive common environmental stresses such as desiccation and nutrient limitation. This mode of life is often essential for survival in bacteria of the genera Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Rhizobium. The role of biofilm formation in symbiosis has been investigated in detail for Sinorhizobium meliloti and Bradyrhizobium japonicum. However, for S. fredii this process has not been studied. In this work we have demonstrated that biofilm formation is crucial for an optimal root colonization and symbiosis between S. fredii SMH12 and Glycine max cv Osumi. In this bacterium, nod-gene inducing flavonoids and the NodD1 protein are required for the transition of the biofilm structure from monolayer to microcolony. Quorum Sensing systems are also required for the full development of both types of biofilms. In fact, both the nodD1 mutant and the lactonase strain (the lactonase enzyme prevents AHL accumulation are defective in soybean root colonization. The impairment of the lactonase strain in its colonization ability leads to a decrease in the symbiotic parameters. Interestingly, NodD1 together with flavonoids activates certain quorum sensing systems implicit in the development of the symbiotic biofilm. Thus, S. fredii SMH12 by means of a unique key molecule, the flavonoid, efficiently forms biofilm, colonizes the legume roots and activates the synthesis of Nod factors, required for successfully symbiosis.

  20. Waterlogging tolerance, tissue nitrogen and oxygen transport in the forage legume Melilotus siculus: a comparison of nodulated and nitrate-fed plants.

    Science.gov (United States)

    Konnerup, Dennis; Toro, Guillermo; Pedersen, Ole; Colmer, Timothy David

    2018-01-17

    Soil waterlogging adversely impacts most plants. Melilotus siculus is a waterlogging-tolerant annual forage legume, but data were lacking for the effects of root-zone hypoxia on nodulated plants reliant on N2 fixation. The aim was to compare the waterlogging tolerance and physiology of M. siculus reliant on N2 fixation or with access to NO3-. A factorial experiment imposed treatments of water level (drained or waterlogged), rhizobia (nil or inoculated) and mineral N supply (nil or 11 mm NO3-) for 21 d on plants in pots of vermiculite in a glasshouse. Nodulation, shoot and root growth and tissue N were determined. Porosity (gas volume per unit tissue volume) and respiration rates of root tissues and nodules, and O2 microelectrode profiling across nodules, were measured in a second experiment. Plants inoculated with the appropriate rhizobia, Ensifer (syn. Sinorhizobium) medicae, formed nodules. Nodulated plants grew as well as plants fed NO3-, both in drained and waterlogged conditions. The growth and total N content of nodulated plants (without any NO3- supplied) indicated N2 fixation. Respiration rates (mass basis) were highest in nodules and root tips and lowest in basal root tissues. Secondary aerenchyma (phellem) formed along basal root parts and a thin layer of this porous tissue also covered nodules, which together enhanced gas-phase diffusion of O2 to the nodules; O2 was below detection within the infected zone of the nodule interior. Melilotus siculus reliant on N2 fixation grew well both in drained and waterlogged conditions, and had similar tissue N concentrations. In waterlogged conditions the relatively high respiration rates of nodules must rely on O2 movement via the aerenchymatous phellem in hypocotyl, roots and the outer tissue layers of nodules. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China.

    Science.gov (United States)

    Wu, Li Juan; Wang, Hai Qing; Wang, En Tao; Chen, Wen Xin; Tian, Chang Fu

    2011-06-01

    A total of 99 bacterial isolates that originated from root nodules of Glycine soja were characterized with restriction analyses of amplified 16S ribosomal DNA and 16S-23S rDNA intergenic spacers (ITS), and sequence analyses of 16S rRNA, rpoB, atpD, recA and nodC genes. When tested for nodulation of G. soja, 72 of the isolates were effective symbionts, and these belonged to five species: Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense and Sinorhizobium fredii. All of these, except some B. yuanmingense strains, also formed effective nodules on the domesticated soybean Glycine max. The remaining 27 isolates did not nodulate either host, but were identified as Rhizobium. Phylogeny nodC in the G. soja symbionts suggested that this symbiosis gene was mainly maintained by vertical gene transfer. Different nodC sublineages and rrs-ITS clusters reflected the geographic origins of isolates in this study. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  2. Nodulation and Rhizobium Population in Root Nodules of Selected ...

    African Journals Online (AJOL)

    Nodulation and rhizobium population in root nodules of 5- year old Leucaena leucocephala; Gliricidia sepium and Acacia mangium were assessed. Nodules of these tree legumes were quantified in terms of their numbers, lateral and vertical distribution while the rhizobium population in cultured nodules was counted as ...

  3. Diversity of root nodule bacteria from leguminous crops

    Directory of Open Access Journals (Sweden)

    Agrawal Pooja

    2016-01-01

    Full Text Available In the present study, a total of 353 nodule-associated bacteria were isolated from 220 legume plant samples belonging to Cicer arietinum (85, Glycine max (74, Vigna radiata (21 and Cajanus cajan (40. A total of 224 bacteria were identified as fast-growing Rhizobium spp. on the basis of differential staining (Gram staining and carbol fuchsin staining and biochemical tests. All the isolates were tested for indole acetic acid production (IAA, phosphate solubilization and siderophore production on plate assay. To examine the effect of volatile organic metabolites (VOM and water soluble soil components (WSSC on nodule bacteria, culture conditions were optimized by observing the effects of various parameters such as pH, salt content and temperatures on the growth of bacteria. Selected rhizobia were subjected to random amplified polymorphic DNA (RAPD and amplified ribosomal DNA restriction analysis (ARDRA analysis to identify their species. On the basis of RAPD and ARDRA, 10 isolates were identified as Rhizobium meliloti. In this study, Rhizobium GO4, G16, G20, G77, S43, S81, M07, M37, A15 and A55 were observed as the best candidates among the tested bacteria and can be further used as potent bioinoculants.

  4. Molecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.

    Directory of Open Access Journals (Sweden)

    Bénédicte Lafay

    2007-03-01

    Full Text Available Symbiotic relationships between leguminous plants (family Fabaceae and nodule-forming bacteria in Australia native ecosystems remain poorly characterized despite their importance. Most studies have focused on temperate parts of the country, where the use of molecular approaches have already revealed the presence of Bradyrhizobium, Ensifer (formerly Sinorhizobium, Mesorhizobium and Rhizobium genera of legume root-nodule bacteria. We here provide the first molecular characterization of nodulating bacteria from tropical Australia.45 nodule-forming bacterial strains, isolated from eight native legume hosts at eight locations in Kakadu National Park, Northern Territory, Australia, were examined for their genetic diversity and phylogenetic position. Using SSU rDNA PCR-RFLPs and phylogenetic analyses, our survey identified nine genospecies, two of which, Bradyrhizobium genospp. B and P, had been previously identified in south-eastern Australia and one, Mesorhizobium genospecies AA, in southern France. Three of the five newly characterized Bradyrhizobium genospecies were more closely related to B. japonicum USDA110, whereas the other two belonged to the B. elkanii group. All five were each more closely related to strains sampled in various tropical areas outside Australia than to strains known to occur in Australia. We also characterized an entirely novel nodule-forming lineage, phylogenetically distant from any previously described rhizobial and non-rhizobial legume-nodulating lineage within the Rhizobiales.Overall, the present results support the hypothesis of tropical areas being centres of biodiversity and diversification for legume root-nodule bacteria and confirm the widespread occurrence of Bradyrhizobium genosp. B in continental Australia.

  5. A thaumatin-like protein, Rj4, controls nodule symbiotic specificity in soybean.

    Science.gov (United States)

    Hayashi, Masaki; Shiro, Sokichi; Kanamori, Hiroyuki; Mori-Hosokawa, Satomi; Sasaki-Yamagata, Harumi; Sayama, Takashi; Nishioka, Miki; Takahashi, Masakazu; Ishimoto, Masao; Katayose, Yuichi; Kaga, Akito; Harada, Kyuya; Kouchi, Hiroshi; Saeki, Yuichi; Umehara, Yosuke

    2014-09-01

    Soybeans exhibit a nitrogen-fixing symbiosis with soil bacteria of the genera Bradyrhizobium and Ensifer/Sinorhizobium in a unique organ, the root nodule. It is well known that nodulation of soybean is controlled by several host genes referred to as Rj (rj) genes. Among these genes, a dominant allele, Rj4, restricts nodulation with specific bacterial strains such as B. elkanii USDA61 and B. japonicum Is-34. These incompatible strains fail to invade the host epidermal cells as revealed by observations using DsRed-labeled bacteria. Here, we describe the molecular identification of the Rj4 gene by using map-based cloning with several mapping populations. The Rj4 gene encoded a thaumatin-like protein (TLP) that belongs to pathogenesis-related (PR) protein family 5. In rj4/rj4 genotype soybeans and wild soybeans, we found six missense mutations and two consecutive amino acid deletions in the rj4 gene as compared with the Rj4 allele. We also found, using hairy root transformation, that the rj4/rj4 genotype soybeans were fully complemented by the expression of the Rj4 gene. Whereas the expression of many TLPs and other PR proteins is induced by biotic/abiotic stress, Rj4 gene expression appears to be constitutive in roots including root nodules. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes.

    Science.gov (United States)

    Gage, Daniel J

    2004-06-01

    Bacteria belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. The interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. Temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that arise from root inner and middle cortical cells and grow out from the root via a persistent meristem. During the formation of functional indeterminate nodules, symbiotic bacteria must gain access to the interior of the host root. To get from the outside to the inside, rhizobia grow and divide in tubules called infection threads, which are composite structures derived from the two symbiotic partners. This review focuses on symbiotic infection and invasion during the formation of indeterminate nodules. It summarizes root hair growth, how root hair growth is influenced by rhizobial signaling molecules, infection of root hairs, infection thread extension down root hairs, infection thread growth into root tissue, and the plant and bacterial contributions necessary for infection thread formation and growth. The review also summarizes recent advances concerning the growth dynamics of rhizobial populations in infection threads.

  7. The Sinorhizobium fredii HH103 MucR1 Global Regulator Is Connected With the nod Regulon and Is Required for Efficient Symbiosis With Lotus burttii and Glycine max cv. Williams.

    Science.gov (United States)

    Acosta-Jurado, Sebastián; Alias-Villegas, Cynthia; Navarro-Gómez, Pilar; Zehner, Susanne; Murdoch, Piedad Del Socorro; Rodríguez-Carvajal, Miguel A; Soto, María J; Ollero, Francisco-Javier; Ruiz-Sainz, José E; Göttfert, Michael; Vinardell, José-María

    2016-09-01

    Sinorhizobium fredii HH103 is a rhizobial strain showing a broad host range of nodulation. In addition to the induction of bacterial nodulation genes, transition from a free-living to a symbiotic state requires complex genetic expression changes with the participation of global regulators. We have analyzed the role of the zinc-finger transcriptional regulator MucR1 from S. fredii HH103 under both free-living conditions and symbiosis with two HH103 host plants, Glycine max and Lotus burttii. Inactivation of HH103 mucR1 led to a severe decrease in exopolysaccharide (EPS) biosynthesis but enhanced production of external cyclic glucans (CG). This mutant also showed increased cell aggregation capacity as well as a drastic reduction in nitrogen-fixation capacity with G. max and L. burttii. However, in these two legumes, the number of nodules induced by the mucR1 mutant was significantly increased and decreased, respectively, with respect to the wild-type strain, indicating that MucR1 can differently affect nodulation depending on the host plant. RNA-Seq analysis carried out in the absence and the presence of flavonoids showed that MucR1 controls the expression of hundreds of genes (including some related to EPS production and CG transport), some of them being related to the nod regulon.

  8. The stress-related, rhizobial small RNA RcsR1 destabilizes the autoinducer synthase encoding mRNA sinI in Sinorhizobium meliloti

    Czech Academy of Sciences Publication Activity Database

    Baumgardt, K.; Šmídová, Klára; Rahn, H.; Lochnit, G.; Robledo, M.; Evguenieva-Hackenberg, E.

    2016-01-01

    Roč. 13, č. 5 (2016), s. 486-499 ISSN 1547-6286 Institutional support: RVO:61388971 Keywords : Agrobacterium * autoinducer synthase * degradosome Subject RIV: EE - Microbiology, Virology Impact factor: 3.900, year: 2016

  9. A 13C-NMR study of exopolysaccharide synthesis in Rhizobium meliloti Su47 strain

    Science.gov (United States)

    Tavernier, P.; Portais, J.-C.; Besson, I.; Courtois, J.; Courtois, B.; Barbotin, J.-N.

    1998-02-01

    Metabolic pathways implied in the synthesis of succinoglycan produced by the Su47 strain of R. meliloti were evaluated by 13C-NMR spectroscopy after incubation with [1{-}13C] or [2{-}13C] glucose. The biosynthesis of this polymer by R. meliloti from glucose occurred by a direct polymerisation of the introduced glucose and by the pentose phosphate pathway. Les voies métaboliques impliquées dans la synthèse du succinoglycane produit par la souche Su47 de R. meliloti ont été évaluées par la spectroscopie de RMN du carbone 13 après incubation des cellules avec du [1{-}13C] ou [2{-}13C] glucose. La biosynthèse de ce polymère à partir du glucose se produit par polymérisation directe du glucose et par la voie des pentoses phosphate.

  10. NODUL TIROID SOLITER

    Directory of Open Access Journals (Sweden)

    I Gusti Ayu Prema Yani Sidemen

    2014-10-01

    Full Text Available Latar Belakang: Nodul tiroid adalah pembengkakan atau massa pada kelenjar tiroid.Pembedahan merupakan pilihan terapi utama, namun pembedahan yang tidak dilakukandengan baik berisiko tinggi mencederai 2 struktur penting, yakni kelenjar paratiroid dannervus rekuren laringeal. Risiko nodul tiroid akan meningkat seiring pertambahan usiadan kurangnya asupan sodium.Insiden terjadinya nodul tiroid lebih sering ditemukanpada laki-laki dan usia di atas 50 tahun, namun pada kasus ini nodul tiroid soliterditemukan pada seorang perempuan dewasa muda sehingga melatar belakangi penulisuntuk mendiskusikan kasus ini dalam laporan kasus.Kasus: Seorang pasien perempuan 32 tahun dengan keluhan tumbuh benjolan padaleher kiri sejak ± 1 tahun yang lalu. Benjolan tersebut dirasakan semakin membesar.Pasien tidak mengeluhkan rasa nyeri di daerah benjolan. Gangguan pada saat makanataupun minum, riwayat sesak, dada berdebar-debar, sering berkeringat, ataupunpenurunan berat badan disangkal. Pada pemeriksaan fisik didapatkan keadaan umumdalam batas normal.  Pada pemeriksaan status lokalis pada region colli anterior lateralsinistra ditemukan massa lunak yang mobile dengan batas tegas dan ukuran ± 3,2 cm x3,4 cm.Hasil: Hasil pemeriksaan patologi anatomi menunjukkan terdapat degenerasi kistikpada massa tiroid tersebut. Pasien kemudian menjalani tindakan pembedahan, yaknitiroidektomi dengan isthmolobectomy. Tiroidektomi dengan teknik diseksi kapsularpada pasien ini berhasil dibuktikan dengan tidak terdapatnya kerusakan pita suara ataukejang pasca operasi.Kesimpulan: Kondisi pasca tiroidektomi dengan teknik diseksi kapsular pada pasien inibaik, tidak terdapat komplikasi kerusakan pita suara dan nervus rekuren laringeal,pasien hidup, dan luka operasi terawat baik.

  11. Degradation of phenanthrene by the rhizobacterium Ensifer meliloti.

    Science.gov (United States)

    Muratova, Anna; Pozdnyakova, Natalya; Makarov, Oleg; Baboshin, Mikhail; Baskunov, Boris; Myasoedova, Nina; Golovleva, Ludmila; Turkovskaya, Olga

    2014-11-01

    The biodegradation of the polycyclic aromatic hydrocarbon phenantherene by the rhizobacterial strain Ensifer meliloti P221, isolated from the root zone of plant grown in PAH-contaminated soil was studied. Bacterial growth and phenanthrene degradation under the influence of root-exuded organic acids were also investigated. Analysis of the metabolites produced by the strain by using thin-layer chromatography, gas chromatography, high-pressure liquid chromatography, and mass-spectrometry revealed that phenanthrene is bioconverted via two parallel pathways. The first, major pathway is through terminal aromatic ring cleavage (presumably at the C3-C4 bond) producing benzocoumarin and 1-hydroxy-2-naphthoic acid, whose further degradation with the formation of salicylic acid is difficult or is very slow. The second pathway is through the oxidation of the central aromatic ring at the C9-C10 bond, producing 9,10-dihydro-9,10-dihydroxyphenanthrene, 9,10-phenanthrenequinone, and 2,2'-diphenic acid. This is the first time that the dioxygenation of phenanthrene at the C9 and C10 atoms, proven by identification of characteristic metabolites, has been reported for a bacterium of the Ensifer genus.

  12. Identification of Salt-Tolerant Sinorhizobium sp Strain BL3 Membrane Proteins Based on Proteomics

    DEFF Research Database (Denmark)

    Tanthanuch, Waraporn; Mohammed, Shabaz; Matthiesen, Rune

    2010-01-01

    Sinorhizobium sp. BL3 is a salt-tolerant strain that can fix atmospheric nitrogen in symbiosis with leguminous host plants under salt-stress conditions. Since cell membranes are the first barrier to environmental change, it is interesting to explore the membrane proteins within this protective...

  13. Thyroid carcinoma and hot nodule

    Energy Technology Data Exchange (ETDEWEB)

    Fukata, Shuji; Tamai, Hajime; Matsubayashi, Sunao; Nagai, Keisuke; Hirota, Yoshihiko; Matsuzuka, Fumio; Katayama, Shoichi; Kuma, Kanji; Nagataki, Shigenobu

    1987-09-01

    A 70-year-old woman presented with a nodule in the thyroid gland. /sup 131/I scintigraphy of the gland showed a hot nodule. Histology of the resected thyroid revealed a papillary adenocarcinoma. Although a thyroid carcinoma with a hot nodule seen on the radioiodine isotope scan is a very rare occurrence, it is clinically very important because it may indicate a thyroid malignancy.

  14. The Effect of Indigenous Root-Nodulating Bacteria on Nodulation ...

    African Journals Online (AJOL)

    This study was initiated to isolate and characterize indigenous rhizobia nodulating faba bean, and evaluate symbiotic characteristics between the crop and the rhizobia in major faba bean producing areas in Tigray highlands. Field crops were also surveyed for nodulation in selected sites of seven (7) faba bean growing ...

  15. Rhizobium helanshanense sp. nov., a bacterium that nodulates Sphaerophysa salsula (Pall.) DC. in China.

    Science.gov (United States)

    Qin, Wei; Deng, Zhen Shan; Xu, Lin; Wang, Na Na; Wei, Ge Hong

    2012-05-01

    Studying rhizobia in the root nodules of Sphaerophysa salsula (Pall.) DC in the northwest of China, we obtained five strains classified as genus Rhizobium on the basis of their 16S rRNA gene sequences. The sequence similarity of strain CCNWQTX14(T) with the most related species was 99.0%. Further phylogenetic analysis of housekeeping genes (recA and atpD) suggested the five strains comprised a novel lineage within Rhizobium. The nifH and nodD gene sequences of CCNWQTX14(T) were phylogenetically closely related with those of Sinorhizobium kummerowiae and R. sphaerophysae, respectively. The five strains isolated from different places were also distinct from related Rhizobium species using ERIC fingerprint profiles. The DNA-DNA hybridization value was 41.8% between CCNWQTX14(T) and Rhizobium sphaerophysae CCNWGS0238(T). Our novel strains were only able to form effective nodules on its original host Sphaerophysa salsula. Our data showed that the five Rhizobium strains formed a unique genomic species, for which a novel species Rhizobium helanshanense sp. nov. is proposed. The type strain is CCNWQTX14(T) (=ACCC 16237(T) =HAMBI 3083(T)).

  16. Nodules size: An important factor in nodule mining?

    Digital Repository Service at National Institute of Oceanography (India)

    Valsangkar, A.B.

    . In order to minimize ecological and environmental problems, it is emphasized that the nodules should be screened on sea bottom during mining, which may be possible by future technological modification of mining devises...

  17. [Nodulation competitiveness of nodule bacteria: Genetic control and adaptive significance].

    Science.gov (United States)

    Onishchuk, O P; Vorobyov, N I; Provorov, N A

    2017-01-01

    The most recent data on the system of cmp (competitiveness) genes that determine the nodulation competitiveness of rhizobial strains, i.e., the ability to compete for nodule formation in leguminous plants, is analyzed. Three genetic approaches for the construction of economically valuable strains of rhizobia are proposed: the amplification of positive regulators of competitiveness, the inactivation of the negative regulators of this trait, and the introduction of efficient competitiveness factors into strains capable of active nitrogen fixation.

  18. Sucrose synthase and enolase expression in actinorhizal nodules of Alnus glutinosa: comparison with legume nodules.

    NARCIS (Netherlands)

    Ghelue, van M.; Ribeiro, A.; Solheim, B.; Akkermans, A.D.L.; Bisseling, T.; Pawlowski, K.

    1996-01-01

    Abstract Two different types of nitrogen-fixing root nodules are known - actinorhizal nodules induced by Frankia and legume nodules induced by rhizobia. While legume nodules show a stem-like structure with peripheral vascular bundles, actinorhizal nodule lobes resemble modified lateral roots with a

  19. Red nodule on the breast

    Directory of Open Access Journals (Sweden)

    Roberta Colucci

    2012-01-01

    Full Text Available A 63-year-old woman living in the countryside referred to our department with a 2-month history of a red nodule localized on the right breast. Histological examination, immunohistochemical analyses and serologic evaluation conducted with ELISA and Western blot were performed. Clinical diagnosis of borrelial lymphocytoma was not possible solely on the clinical presentation of a classical nodular form without lymphoadenopathy. An absence of a referred prior tick bite and a previous or concomitant erythema migrans at clinical presentation rendered a more challenging diagnosis. The fact that the patient lived in the countryside, the appearance of the breast nodule in September, and serologic, histologic, and immunohistochemical analysis facilitated the diagnosis of borrelial lymphocytoma. We report this case to highlight the importance of an investigation of Lyme borreliosis when a patient living in the countryside presents with a red nodule of the nipple and areola.

  20. Host range, symbiotic effectiveness and nodulation competitiveness ...

    African Journals Online (AJOL)

    ERIC-PCR DNA fingerprinting patterns were used to identify the isolates occupying nodules. All the isolates nodulated cowpea, groundnut (Arachis hypogeae) and mungbean (Vigna radiata), but only AII-2-1, AII-3-4 and BIII-2-2 nodulated soybean (Glycine max). Apart from cowpea where all the isolates were effective, there ...

  1. Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization.

    Science.gov (United States)

    Salas, María Eugenia; Lozano, Mauricio Javier; López, José Luis; Draghi, Walter Omar; Serrania, Javier; Torres Tejerizo, Gonzalo Arturo; Albicoro, Francisco Javier; Nilsson, Juliet Fernanda; Pistorio, Mariano; Del Papa, María Florencia; Parisi, Gustavo; Becker, Anke; Lagares, Antonio

    2017-09-01

    Rhizobia are α- and ß-proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature-tagged-Tn5 mutagenesis (STM) we performed a genome-wide screening for Ensifer meliloti genes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca. 80%) are chromosomally located, pointing to the relevance and ancestral origin of the bacterial ability to colonize plant roots. The identified genes were related to metabolic functions, transcription, signal transduction, and motility/chemotaxis among other categories; with several ORFs of yet-unknown function. Most remarkably, we identified a subset of genes that impacted more severely the colonization of the roots of alfalfa than of pea. Further analyses using other plant species revealed that such early differential phenotype could be extended to other members of the Trifoliae tribe (Trigonella, Trifolium), but not the Fabeae and Phaseoleae tribes. The results suggest that consolidation of E. meliloti into its current symbiotic state should have occurred in a rhizobacterium that had already been adapted to rhizospheres of the Trifoliae tribe. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  2. [Obtaining of fluorescent-labeled nodule bacteria strains of wild legumes for their detection in vive and in vitro].

    Science.gov (United States)

    Baĭmiev, A Kh; Iamidanov, R S; Matniiazov, R T; Blagova, D K; Baĭmiev, A Kh; Chemeris, A V

    2011-01-01

    A series of expression vectors containing genes of fluorescent proteins TurboGFP and TurboRFP under the phage T5 constitutive promoter regulation, intended for lifetime marking of nodule bacteria is created: a series of vectors based on a broad-host-range replicon BBRI, for marking strains with an expression of reporter gene from a transformed plasmid and a series of vectors based on a plasmid pRL765gfp for marking strains by introduction genes of fluorescent proteins in a bacterial chromosome. It was shown that transformation is the most preferable method of constructions transfer in nodule bacteria cells, as in the presence of mob locus in the vectors necessary for conjugation, exists the possibility of occasional plasmid mobilization and its transition from marked strain cells in other soil bacteria. With application of the created vector constructions we obtained fluorescent tagged strains of Rhizobium sp., Mesorhizobium sp., Ensifer (Sinorhizobium) sp., Bradyrhizobium sp., Phyllobacterium sp., Agrobacterium sp. Also their suitability for experiments in vivo and in vitro is shown.

  3. Automated lung nodule classification following automated nodule detection on CT: A serial approach

    International Nuclear Information System (INIS)

    Armato, Samuel G. III; Altman, Michael B.; Wilkie, Joel; Sone, Shusuke; Li, Feng; Doi, Kunio; Roy, Arunabha S.

    2003-01-01

    We have evaluated the performance of an automated classifier applied to the task of differentiating malignant and benign lung nodules in low-dose helical computed tomography (CT) scans acquired as part of a lung cancer screening program. The nodules classified in this manner were initially identified by our automated lung nodule detection method, so that the output of automated lung nodule detection was used as input to automated lung nodule classification. This study begins to narrow the distinction between the 'detection task' and the 'classification task'. Automated lung nodule detection is based on two- and three-dimensional analyses of the CT image data. Gray-level-thresholding techniques are used to identify initial lung nodule candidates, for which morphological and gray-level features are computed. A rule-based approach is applied to reduce the number of nodule candidates that correspond to non-nodules, and the features of remaining candidates are merged through linear discriminant analysis to obtain final detection results. Automated lung nodule classification merges the features of the lung nodule candidates identified by the detection algorithm that correspond to actual nodules through another linear discriminant classifier to distinguish between malignant and benign nodules. The automated classification method was applied to the computerized detection results obtained from a database of 393 low-dose thoracic CT scans containing 470 confirmed lung nodules (69 malignant and 401 benign nodules). Receiver operating characteristic (ROC) analysis was used to evaluate the ability of the classifier to differentiate between nodule candidates that correspond to malignant nodules and nodule candidates that correspond to benign lesions. The area under the ROC curve for this classification task attained a value of 0.79 during a leave-one-out evaluation

  4. 10Be in manganese nodules

    International Nuclear Information System (INIS)

    Thomas, J.; Parker, P.; Mangini, A.; Cochran, K.; Turekian, K.; Krishnaswami, S.; Sharma, P.

    1981-01-01

    10 Be (t/sub 1/2) = 1.5 MY) is(formed in the upper atmosphere by cosmic ray spallation on nitrogen and oxygen. It is transported to the earth's surface via precipitation. In the oceans it is eventually associated with solid phases depositing on the ocean floor such as manganese nodules and deep-sea sediments. One of the assumptions that is normally made in analysis of such processes is that 10 Be has been produced at a relatively uniform rate over the pat several million years. If we assume, in addition, that the initial specific concentration of 10 Be as it precipitates with a solid phase is invariant with time, then we would expect that the decrease of the 10 Be concentration as a function of depth in a deep-sea core or in a manganese nodule would provide a record of sediment accumulation rate in the former and of growth rate in the latter. The possibility of using cosmic-ray produced 10 Be for the dating of marine deposits had been proposed 25 years ago by Arnold and Goel et al. The method of analysis used by these investigators, and those subsequently pursuing the problem, was low-level β counting. Though the potential of using 10 Be for dating manganese nodules was explored more than a decade ago, only a few measurements of 10 Be in nodules exist in date. This is largely because of the 10 Be measurements in environmental samples have gained considerable momentum during the past 3 to 4 years, after the development of accelerator mass spectrometry for its determination

  5. Pulmonary nodules: detection, assessment, and CAD.

    Science.gov (United States)

    Girvin, Francis; Ko, Jane P

    2008-10-01

    The imaging of pulmonary nodules is an evolving and dynamic field. In this review, we discuss the detection and multitechnique characterization of pulmonary nodules, emphasizing the impact of technological advances on both noninvasive and invasive evaluation and surveillance. The potential contribution of MRI, evolving imaging-guided techniques, and computer applications are also discussed. Advances in MDCT and PET and the potential contribution of fast-imaging MRI sequences and computer applications should continue to improve our evaluation of the solitary pulmonary nodule.

  6. Cytological diagnosis of microfilariae in subcutaneous nodule

    Directory of Open Access Journals (Sweden)

    Narayanan K Panicker

    2012-01-01

    Full Text Available Microfilariaemia presenting with subcutaneous nodule is rare. We report a case of a 22-year-old female patient who presented with a subcutaneous nodule on right forearm. Fine-needle aspiration cytology from the nodule showed many sheathed motile microfilaria on wet mount preparation during day time. Wuchereria loa loa is known to be associated with soft tissue swellings as reported earlier. Nocturnal motility and cytomorphological features differentiate Wuchereria bancrofti from Wuchereria loa loa.

  7. Auxin transport, metabolism, and signalling during nodule initiation: indeterminate and determinate nodules

    NARCIS (Netherlands)

    Kohlen, W.; Ng, Jason Liang Pin; Deinum, E.E.; Mathesius, Ulrike

    2018-01-01

    Most legumes can form a unique type of lateral organ on their roots: root nodules. These structures host symbiotic nitrogen-fixing bacteria called rhizobia. Several different types of nodules can be found in nature, but the two best-studied types are called indeterminate and determinate nodules.

  8. Lactose inhibits the growth of Rhizobium meliloti cells that contain an actively expressed Escherichia coli lactose operon.

    Science.gov (United States)

    Timblin, C R; Kahn, M L

    1984-01-01

    Expression of the Escherichia coli lactose operon in Rhizobium meliloti 104A14 made the cells sensitive to the addition of the beta-galactosides lactose, phenyl-beta-D-galactoside, and lactobionic acid. Growth stopped when the beta-galactoside was added and viability decreased modestly during the next few hours, but little cell lysis was observed and the cells appeared normal. Protein synthesis was not inhibited. Growth was inhibited only when beta-galactosidase expression was greater than 160 U. Lactose-resistant mutants had defects in the plasmid-carried E. coli beta-galactosidase or beta-galactoside permease and in the R. meliloti genome. We speculate that uncontrolled production of galactose by the action of the lactose operon proteins was responsible for growth inhibition. PMID:6427192

  9. Strategy for polymetallic nodule mining

    Digital Repository Service at National Institute of Oceanography (India)

    Sharma, R.

    'Jrlii, SinL:C tbe economic viahility of deep sCnodules and sulfides are being looked upon as an alternative tu the existing but fast dwindling land rcsourccs. Land reseNcs of... and dcscrib\\:s the approach for delineation of a mine !>itc and collection of baseline dala. 42 tn\\ertUlllQIUII ChaUenaa- VoL 10 N.... 3 • 1990 Criteria for delineation of mine site The term 'minesilc' is defined as an ocean bottom area where underspccifie...

  10. Management of solid pulmonary nodules

    International Nuclear Information System (INIS)

    Poschenrieder, F.; Beyer, L.; Stroszczynski, C.; Hamer, O.W.; Rehbock, B.; Diederich, S.; Wormanns, D.

    2014-01-01

    The increasing availability of computed tomography has meant that the number of incidentally detected solitary pulmonary nodules (SPN) has greatly increased in recent years. A reasonable management of these SPN is necessary in order to firstly be able to detect malignant lesions early on and secondly to avoid upsetting the patient unnecessarily or carrying out further stressful diagnostic procedures. This review article shows how the dignity of SPNs can be estimated and based on this how the management can be accomplished taking established guidelines into consideration. (orig.) [de

  11. Lactose inhibits the growth of Rhizobium meliloti cells that contain an actively expressed Escherichia coli lactose operon.

    OpenAIRE

    Timblin, C R; Kahn, M L

    1984-01-01

    Expression of the Escherichia coli lactose operon in Rhizobium meliloti 104A14 made the cells sensitive to the addition of the beta-galactosides lactose, phenyl-beta-D-galactoside, and lactobionic acid. Growth stopped when the beta-galactoside was added and viability decreased modestly during the next few hours, but little cell lysis was observed and the cells appeared normal. Protein synthesis was not inhibited. Growth was inhibited only when beta-galactosidase expression was greater than 16...

  12. ORF Alignment: NC_003037 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available n with ... localized conservation [Sinorhizobium meliloti 1021] ... pir||B95312 hypothetical p...rvation [Sinorhizobium ... meliloti 1021] gb|AAK65060.1| hypothetical protei... NC_003037 gi|16262858 >1i0rB 4 152 13 156 2e-27 ... ref|NP_435648.1| hypothetical protein with localized conse

  13. ORF Alignment: NC_003037 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available n with ... localized conservation [Sinorhizobium meliloti 1021] ... pir||B95312 hypothetical p...rvation [Sinorhizobium ... meliloti 1021] gb|AAK65060.1| hypothetical protei... NC_003037 gi|16262855 >1i0rB 4 152 13 156 2e-27 ... ref|NP_435648.1| hypothetical protein with localized conse

  14. ORF Alignment: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003047 gi|15964777 >1v4aA 24 435 49 467 e-101 ... emb|CAC45596.1| PUTATIVE GLUTAMATE-AMMONIA...-LIGASE ADENYLYLTRANSFERASE PROTEIN ... [Sinorhizobium meliloti] ref|NP_385130.1| PUTATIVE ... GLUTAMATE-AMMO...NIA-LIGASE ADENYLYLTRANSFERASE PROTEIN ... [Sinorhizobium meliloti 1021] sp|

  15. Indeterminate Pulmonary Nodules at Colorectal Cancer Staging

    DEFF Research Database (Denmark)

    Nordholm-Carstensen, Andreas; Wille-Jørgensen, Peer A; Jorgensen, Lars N

    2013-01-01

    This study aimed to estimate the prevalence of indeterminate pulmonary nodules and specific radiological and clinical characteristics that predict malignancy of these at initial staging chest computed tomography (CT) in patients with colorectal cancer. A considerable number of indeterminate...... pulmonary nodules, which cannot readily be classified as either benign or malignant, are detected at initial staging chest CT in colorectal cancer patients....

  16. Position of solitary thyroid nodules by gammagraphy

    International Nuclear Information System (INIS)

    Basteris M, J.; Gomez D, R.

    2007-01-01

    In this work it is presented which it is the position more frequent of the solitary thyroid nodules. It was used the method of retrospective longitudinal observational investigation in 125 patients that went to the laboratory for realization of detection of thyroid nodules in the years 2004 and 2005 through gammagraphy. (Author)

  17. “Ménage à trois”: the presence/absence of thyme shapes the mutualistic interaction between the host plant Medicago truncatula (Fabaceae) and its symbiotic bacterium Sinorhizobium meliloti

    DEFF Research Database (Denmark)

    Ehlers, Bodil Kirstine; Grøndahl, Eva; Ronfort, Joelle

    2012-01-01

    (carvacrol) leached into the soil by Thymus vulgaris—a common plant of the Mediterranean vegetation, often co-occuring with Medicago. We show that the presence of carvacrol in the soil dramatically affects fitness of the rhizobial partner and increases the magnitude of rG between plant and rhizobia fitness...

  18. The structure of Sinorhizobium meliloti phage ΦM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages.

    Science.gov (United States)

    Stroupe, M Elizabeth; Brewer, Tess E; Sousa, Duncan R; Jones, Kathryn M

    2014-02-01

    ΦM12 is the first example of a T=19l geometry capsid, encapsulating the recently sequenced genome. Here, we present structures determined by cryo-EM of full and empty capsids. The structure reveals the pattern for assembly of 1140 HK97-like capsid proteins, pointing to interactions at the pseudo 3-fold symmetry axes that hold together the asymmetric unit. The particular smooth surface of the capsid, along with a lack of accessory coat proteins encoded by the genome, suggest that this interface is the primary mechanism for capsid assembly. Two-dimensional averages of the tail, including the neck and baseplate, reveal that ΦM12 has a relatively narrow neck that attaches the tail to the capsid, as well as a three-layer baseplate. When free from DNA, the icosahedral edges expand by about 5nm, while the vertices stay at the same position, forming a similarly smooth, but bowed, T=19l icosahedral capsid. © 2013 Elsevier Inc. All rights reserved.

  19. Benign solitary solid cold thyroid nodules

    DEFF Research Database (Denmark)

    Døssing, Helle; Bennedbaek, Finn Noe; Karstrup, Steen

    2002-01-01

    PURPOSE: To evaluate the effects of ultrasonography (US)-guided interstitial laser photocoagulation (ILP) on the volume of benign solitary solid cold thyroid nodules and any nodule-related symptoms. MATERIALS AND METHODS: ILP was performed in 16 patients with normal thyroid function and a solid...... benign thyroid nodule. None of the patients had uptake on a radionuclide scan. Patients underwent one ILP session. A needle was positioned in the thyroid nodule with US guidance, and the laser fiber was placed in the lumen of the needle. Patients were treated for 287-1,200 seconds with an output power...... of 1-3 W. ILP was performed with continuous US guidance and terminated when the echogenic changes were stationary. Thyroid nodule volume and thyroid function were evaluated before and 1, 3, and 6 months after treatment. During the same period, 15 untreated patients (control group) were followed up...

  20. Improved Drought Stress Response in Alfalfa Plants Nodulated by an IAA Over-producing Rhizobium Strain

    Directory of Open Access Journals (Sweden)

    Roberto Defez

    2017-12-01

    Full Text Available The drought–stress response in plant involves the cross-talk between abscisic acid (ABA and other phytohormones, such as jasmonates and ethylene. The auxin indole-3-acetic acid (IAA plays an integral part in plant adaptation to drought stress. Investigation was made to see how the main auxin IAA interacted with other plant hormones under water stress, applied through two different growth conditions (solid and hydroponic. Medicago sativa plants nodulated by the Ensifer meliloti wild type 1021 (Ms-1021 and its IAA-overproducing RD64 derivative strains (Ms-RD64 were subjected to drought stress, comparing their response. When the expression of nifH gene and the activity of the nitrogenase enzyme were measured after stress treatments, Ms-RD64 plants recorded a significantly weaker damage. These results were correlated with a lower biomass reduction, and a higher Rubisco protein level measured for the Ms-RD64-stressed plants as compared to the Ms-1021-stressed ones. It has been verified that the stress response observed for Ms-RD64-stressed plants was related to the production of greater amount of low-molecular-weight osmolytes, such as proline and pinitol, measured in these plants. For the Ms-RD64 plants the immunoblotting analysis of thylakoid membrane proteins showed that some of the photosystem proteins increased after the stress. An increased non-photochemical quenching after the stress was also observed for these plants. The reduced wilting signs observed for these plants were also connected to the significant down-regulation of the MtAA03 gene involved in the ABA biosynthesis, and with the unchanged expression of the two genes (Mt-2g006330 and Mt-8g095330 of ABA signaling. When the expression level of the ethylene-signaling genes was evaluated by qPCR analysis no significant alteration of the key positive regulators was recorded for Ms-RD64-stressed plants. Coherently, these plants accumulated 40% less ethylene as compared to Ms-1021-stressed

  1. Nitrogen assimilation in soybean nodules, 1

    International Nuclear Information System (INIS)

    Ohyama, Takuji; Kumazawa, Kikuo

    1980-01-01

    In order to elucidate the pathways to assimilate the ammonia produced by N 2 -fixation in soybean nodules, 15 N-labeled compounds were administered to intact nodules or nodule slices pretreated with various inhibitors of nitrogen assimilation. After exposure to 15 N 2 , 15 N-incorporation into various nitrogenous compounds was investigated in attached nodules injected with methionine sulfoximine (MSX) or azaserine (AS). MSX treatment increased the 15 N content of ammonia more than 6 times, however, depressed 15 N content of most of amides and amino acids. AS treatment enhanced 15 N content of amido-N of glutamine as well as ammonia, but decreased amino-N of glutamine and most of amino acids. Experiments with nodule slices pretreated with MSX or AS solution and then fed with 15 N-labeled ammonia or amido- 15 N of glutamine showed the same trends. Aminooxyacetate inhibited nitrogen flow from glutamic acid to other amino acids. These results strongly indicate that the ammonia produced by N 2 -fixation is assimilated by GS/GOGAT system to glutamic acid and then transaminated to various amino acids in situ. 15 N-incorporation patterns in nodule slices fed with 15 N-labeled ammonia, hydroxylamine, nitrite were similar, but nitrate seemed to be reduced in a definite compartment and assimilated similarly as in intact nodules fed with 15 N 2 (author)

  2. Management of a solitary thyroid nodule

    International Nuclear Information System (INIS)

    Rao, R.S.

    1999-01-01

    Solitary nodule in the thyroid is a common clinical entity. A careful clinical assessment is the crucial first step in deciding the modality of treatment. The only worthwhile investigation is FNAC. Other investigations are done merely for the sake of a complete academic work up and can usually be dispensed with in most of the cases. Not every solitary nodule requires surgery. The optimum surgery for a solitary nodule is a total lobectomy. The specimen should be subjected to histological examination before recommending further treatment

  3. [Nodules on localized scleroderma or morphea].

    Science.gov (United States)

    Bayle, P; Bazex, J; Marguery, M-C; Lamant, L

    2005-02-01

    Localized scleroderma or morphea usually appears as flat or depressed lesions. We report 3 cases of morphea with atypical appearance, alternating pigmented and depigmented patches with nodules or sclerous bands, occurring in adult men. The occurrence of nodular elements on generalized or localized scleroderma, although rare, was first reported in the literature by Addisson in 1884. These nodules usually appear during evolution. These scleroderma are then described as being keloidal or nodular. We report 3 cases of nodules on localized scleroderma which appeared at the beginning of the dermatosis and where the scleroderma had a similar unusual irregularly pigmented appearance.

  4. effect of exogenous application of rhizopine on lucerne root nodulation

    African Journals Online (AJOL)

    BSN

    Meade, H. M., Long, S. R., Ruvkun, G. B., Brown, S. E., and Ausubel, F. M. (1982). Physical and genetic characterisation of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. Jou ma I of Bacteriology. 149: 114-122. Murphy, P.J., Heycke, N., Banfialvi, Z., Tate, M.E., de Bruijn, ...

  5. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Kimbrel

    2013-02-01

    Full Text Available Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.

  6. Escherichia coli BdcA controls biofilm dispersal in Pseudomonas aeruginosa and Rhizobium meliloti

    Directory of Open Access Journals (Sweden)

    Wood Thomas K

    2011-10-01

    Full Text Available Abstract Background Previously we showed that BdcA controls Escherichia coli biofilm dispersal by binding the ubiquitous bacterial signal cyclic diguanylate (c-di-GMP; upon reducing the concentration of c-di-GMP, the cell shifts to the planktonic state by increasing motility, decreasing aggregation, and decreasing production of biofilm adhesins. Findings Here we report that BdcA also increases biofilm dispersal in other Gram-negative bacteria including Pseudomonas aeruginosa, Pseudomonas fluorescens, and Rhizobium meliloti. BdcA binds c-di-GMP in these strains and thereby reduces the effective c-di-GMP concentrations as demonstrated by increases in swimming motility and swarming motility as well as by a reduction in extracellular polysaccharide production. We also develop a method to displace existing biofilms by adding BdcA via conjugation from E. coli in mixed-species biofilms. Conclusion Since BdcA shows the ability to control biofilm dispersal in diverse bacteria, BdcA has the potential to be used as a tool to disperse biofilms for engineering and medical applications.

  7. Limited Utility of Pulmonary Nodule Risk Calculators for Managing Large Nodules.

    Science.gov (United States)

    Hammer, Mark M; Nachiappan, Arun C; Barbosa, Eduardo J Mortani

    The optimal management of large pulmonary nodules, at higher risk for lung cancer, has not been determined, and it remains unclear as to which patients should undergo follow-up imaging vs invasive tissue diagnosis via biopsy or surgical resection. Through search of radiology reports, 86 nodules from our institution were identified using the inclusion criterion of solid nodules measuring greater than 8mm. We evaluated these nodules with a number of risk prediction calculators, including the Brock University model, and compared these against the proven diagnosis. Of 86 nodules, 59 (69%) nodules were malignant. The most accurate predictive model, the Brock University calculator, underestimated the risk for this group at 33%. At its optimal threshold, this model had a positive predictive value of 81% and negative predictive value of 53%. Notwithstanding the low negative predictive value, the positive predictive value was no better than patients clinically selected for biopsy (86% of biopsies were malignant). Existing nodule risk prediction calculators are of limited usage in guiding the management of large pulmonary nodules. At present, the accuracy of these models in this setting is inferior to expert clinical judgment, and future work is needed to develop management algorithms for higher-risk nodules. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Pulmonary nodules secondary to total parenteral alimentation

    International Nuclear Information System (INIS)

    Landry, B.A.; Melhem, R.E.

    1989-01-01

    A seven-year-old male, who had a retroperitoneal alveolar rhabdomyosarcoma and was on total parenteral alimentation (TPN) developed muliple pulmonary nodules, indistinguishable from metastases. These proved to be multiple lipid emboli on open biopsy. (orig.)

  9. Nodule bottom backscattering study using multibeam echosounder

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Raju, Y.S.N.; Nair, R.R.

    A study is carried out to observe the angular dependence of backscattering strength at nodule area where grab sample and photographic data is available. Theoretical study along with the experimentally observed data shows that the backscattering...

  10. Actinorhizal nitrogen fixing nodules: infection process, molecular ...

    African Journals Online (AJOL)

    Actinorhizal nitrogen fixing nodules: infection process, molecular biology and genomics. Mariana Obertello, Mame Oureye SY, Laurent Laplaze, Carole Santi, Sergio Svistoonoff, Florence Auguy, Didier Bogusz, Claudine Franche ...

  11. Pulmonary nodules secondary to total parenteral alimentation

    Energy Technology Data Exchange (ETDEWEB)

    Landry, B.A.; Melhem, R.E.

    1989-07-01

    A seven-year-old male, who had a retroperitoneal alveolar rhabdomyosarcoma and was on total parenteral alimentation (TPN) developed muliple pulmonary nodules, indistinguishable from metastases. These proved to be multiple lipid emboli on open biopsy. (orig.).

  12. Atypical Localized Rheumatoid Nodule: Case Report

    Directory of Open Access Journals (Sweden)

    KORHAN BARIS BAYRAM

    2015-01-01

    Full Text Available Rheumatoid nodules can be seen in about 30% of patiens with rheumatoid arthritis. They are occasionally localized subcutaneous, but they can rarely seen in visceral organs. Their appearance can be confused with many clinical conditions when they have atypical localizations. To exclude the presence of a malignancy, these lesions should always be investigated. We aimed to discuss a patient with rheumatoid nodule localized in close neighborhood of hyoid bone, presumed as malignancy.

  13. Pulmonary nodule classification with deep residual networks.

    Science.gov (United States)

    Nibali, Aiden; He, Zhen; Wollersheim, Dennis

    2017-10-01

    PURPOSE  : Lung cancer has the highest death rate among all cancers in the USA. In this work we focus on improving the ability of computer-aided diagnosis (CAD) systems to predict the malignancy of nodules from cropped CT images of lung nodules. We evaluate the effectiveness of very deep convolutional neural networks at the task of expert-level lung nodule malignancy classification. Using the state-of-the-art ResNet architecture as our basis, we explore the effect of curriculum learning, transfer learning, and varying network depth on the accuracy of malignancy classification. Due to a lack of public datasets with standardized problem definitions and train/test splits, studies in this area tend to not compare directly against other existing work. This makes it hard to know the relative improvement in the new solution. In contrast, we directly compare our system against two state-of-the-art deep learning systems for nodule classification on the LIDC/IDRI dataset using the same experimental setup and data set. The results show that our system achieves the highest performance in terms of all metrics measured including sensitivity, specificity, precision, AUROC, and accuracy. The proposed method of combining deep residual learning, curriculum learning, and transfer learning translates to high nodule classification accuracy. This reveals a promising new direction for effective pulmonary nodule CAD systems that mirrors the success of recent deep learning advances in other image-based application domains.

  14. Ensifer meliloti overexpressing Escherichia coli phytase gene (appA) improves phosphorus (P) acquisition in maize plants.

    Science.gov (United States)

    Sharma, Vikas; Kumar, Ajit; Archana, G; Kumar, G Naresh

    2016-10-01

    The Escherichia coli phytase gene appA encoding enzyme AppA was cloned in a broad host range plasmid pBBR1MCS2 (lac promoter), termed pVA1, and transformed into the Ensifer meliloti 1020. Transformation of pVA1 in Ensifer meliloti {E. m (pVA1)} increased its phosphatase and phytase activity by ∼9- and ∼50-fold, respectively, compared to the transformants containing empty plasmid as control {E. m (pBBR1MCS2)}. The western blot experiments using rabbit anti-AppA antibody showed that AppA is translocated into the periplasm of the host after its expression. Ensifer meliloti harboring AppA protein {E. m (pVA1)} and {E. m (pBBR1MCS2)} could acidify the unbuffered phytate minimal media (pH 8.0) containing Ca-phytate or Na-phytate as sole organic P (Po) source to below pH 5.0 and released P. However, both {E. m (pVA1)} and {E. m (pBBR1MCS2)} neither dropped pH of the medium nor released P when the medium was buffered at pH 8.0 using Tris-Cl, indicating that acidification of medium was important for the enzymatic hydrolysis of phytate. Further experiments proved that maize plants inoculated with {E. m. (pVA1)} showed increase in growth under sterile semi solid agar (SSA) medium containing Na-phytate as sole P source. The present study could be helpful in generating better transgenic bioinoculants harboring phosphate mineralization properties that ultimately promote plant growth.

  15. Ensifer meliloti overexpressing Escherichia coli phytase gene ( appA) improves phosphorus (P) acquisition in maize plants

    Science.gov (United States)

    Sharma, Vikas; Kumar, Ajit; Archana, G.; Kumar, G. Naresh

    2016-10-01

    The Escherichia coli phytase gene appA encoding enzyme AppA was cloned in a broad host range plasmid pBBR1MCS2 ( lac promoter), termed pVA1, and transformed into the Ensifer meliloti 1020. Transformation of pVA1 in Ensifer meliloti { E. m (pVA1)} increased its phosphatase and phytase activity by ˜9- and ˜50-fold, respectively, compared to the transformants containing empty plasmid as control { E. m (pBBR1MCS2)}. The western blot experiments using rabbit anti-AppA antibody showed that AppA is translocated into the periplasm of the host after its expression. Ensifer meliloti harboring AppA protein { E. m (pVA1)} and { E. m (pBBR1MCS2)} could acidify the unbuffered phytate minimal media (pH 8.0) containing Ca-phytate or Na-phytate as sole organic P (Po) source to below pH 5.0 and released P. However, both { E. m (pVA1)} and { E. m (pBBR1MCS2)} neither dropped pH of the medium nor released P when the medium was buffered at pH 8.0 using Tris-Cl, indicating that acidification of medium was important for the enzymatic hydrolysis of phytate. Further experiments proved that maize plants inoculated with { E. m. (pVA1)} showed increase in growth under sterile semi solid agar (SSA) medium containing Na-phytate as sole P source. The present study could be helpful in generating better transgenic bioinoculants harboring phosphate mineralization properties that ultimately promote plant growth.

  16. "Nodule in Nodule" on Thyroid Ultrasonography: Possibility of Follicular Carcinoma Transformed from Benign Thyroid Tumor.

    Science.gov (United States)

    Kobayashi, Kaoru; Ota, Hisashi; Hirokawa, Mitsuyoshi; Yabuta, Tomonori; Fukushima, Mitsuhiro; Masuoka, Hiroo; Higashiyama, Takuya; Kihara, Minoru; Ito, Yasuhiro; Miya, Akihiro; Miyauchi, Akira

    2017-04-01

    It is generally considered impossible to differentiate follicular carcinomas from follicular adenomas by means of ultrasonography or cytology before surgery. Therefore, follicular carcinoma is histopathologically diagnosed by verifying capsular and/or vascular invasion after surgery. However, ultrasonography may play an important role in diagnosing follicular carcinoma preoperatively in a small number of cases. Four cases of follicular carcinoma or follicular neoplasm that transformed from a benign thyroid tumor and demonstrated a "nodule in nodule" appearance on ultrasonography are presented in this report. Characteristic ultrasound features of such patients are: (1) a "nodule in nodule" appearance, (2) a well-defined boundary line between the nodules, and (3) separate distribution of blood signals within each nodule. A small number of patients with follicular carcinomas or follicular neoplasms may present with a "nodule in nodule" appearance on ultrasonography. It was suggested a long time ago that follicular carcinomas may develop from benign thyroid tumors. The fact that follicular carcinomas appear within benign tumors may be evidence of thyroid tumorigenesis.

  17. The Effects of Clinorotation on the Host Plant, Medicago truncatula, and Its Microbial Symbionts

    Science.gov (United States)

    Dauzart, Ariel; Vandenbrink, Joshua; Kiss, John

    2016-02-01

    Understanding the outcome of the plant-microbe symbiosis in altered gravity is vital to developing life support systems for long-distance space travel and colonization of other planets. Thus, the aim of this research was to understand mutualistic relationships between plants and endophytic microbes under the influence of altered gravity. This project utilized the model tripartite relationship among Medicago truncatula ¬- Sinorhizobium meliloti - Rhizophagus irregularis. Plants were inoculated with rhizobial bacteria (S. meliloti), arbuscular mycorrhizal fungi (R. irregularis), or both microbes, and placed on a rotating clinostat. Vertical and horizontal static controls were also performed. Clinorotation significantly reduced M. truncatula dry mass and fresh mass compared to the static controls. The addition of rhizobia treatments under clinorotation also altered total root length and root-to-shoot fresh mass ratio. Nodule size decreased under rhizobia + clinorotation treatment, and nodule density was significantly decreased compared to the vertical treatment. However, inoculation with arbuscular mycorrhizal fungi was shown to increase biomass accumulation and nodule size. Thus, clinorotation significantly affected M. truncatula and its symbiotic relationships with S. meliloti and R. irregularis. In the long term, the results observed in this clinostat study on the changes of plant-microbe mutualism need to be investigated in spaceflight experiments. Thus, careful consideration of the symbiotic microbes of plants should be included in the design of bioregenerative life support systems needed for space travel.

  18. The Effects of Clinorotation on the Host Plant, Medicago truncatula, and Its Microbial Symbionts

    Directory of Open Access Journals (Sweden)

    Ariel J.C. Dauzart

    2016-02-01

    Full Text Available Understanding the outcome of the plant-microbe symbiosis in altered gravity is vital to developing life support systems for long-distance space travel and colonization of other planets. Thus, the aim of this research was to understand mutualistic relationships between plants and endophytic microbes under the influence of altered gravity. This project utilized the model tripartite relationship among Medicago truncatula ¬– Sinorhizobium meliloti – Rhizophagus irregularis. Plants were inoculated with rhizobial bacteria (S. meliloti, arbuscular mycorrhizal fungi (R. irregularis, or both microbes, and placed on a rotating clinostat. Vertical and horizontal static controls were also performed. Clinorotation significantly reduced M. truncatula dry mass and fresh mass compared to the static controls. The addition of rhizobia treatments under clinorotation also altered total root length and root-to-shoot fresh mass ratio. Nodule size decreased under rhizobia + clinorotation treatment, and nodule density was significantly decreased compared to the vertical treatment. However, inoculation with arbuscular mycorrhizal fungi was shown to increase biomass accumulation and nodule size. Thus, clinorotation significantly affected M. truncatula and its symbiotic relationships with S. meliloti and R. irregularis. In the long term, the results observed in this clinostat study on the changes of plant-microbe mutualism need to be investigated in spaceflight experiments. Thus, careful consideration of the symbiotic microbes of plants should be included in the design of bioregenerative life support systems needed for space travel.

  19. Sonographic scoring of solid thyroid nodules: effects of nodule size and suspicious cervical lymph node

    Directory of Open Access Journals (Sweden)

    Ozlem Unsal

    Full Text Available Abstract Introduction Ultrasound is the most frequently used imaging method to evaluate thyroid nodules. Sonographic characteristics of thyroid nodules which are concerning for malignancy are important to define the need for fine needle aspiration biopsy or open surgery. Objective To evaluate malignancy risk of solid thyroid nodules through sonographic scoring. The effects of nodule size ≥2 cm and associated pathologic cervical lymph node in scoring were examined in addition to generally excepted suspicious features. Methods Medical data of 123 patients underwent thyroid surgery were reviewed, and 89 patients (58 females, 31 males were included in the study. The presence and absence of each suspicious sonographic feature of thyroid nodules were scored as 1 and 0, respectively. Total ultrasound score was obtained by adding the positive ultrasound findings. Differently from the literature, nodule size ≥2 cm and associated pathologic cervical node were added in scoring criteria. The diagnostic performance of nodule characteristics for malignancy and the effect of total US score to discriminate malignant and benign disease were calculated. Results A significant relationship was found between malignancy and hypoechogenity, border irregularity, intranodular vascularity, and microcalcification (p < 0.05. Pathologic cervical node was observed predominantly in association with malignant nodules. Positive predictive value of suspicious cervical node for malignancy was 67%, similar to microcalcification. Nodule size ≥2 cm was not distinctive for diagnosis of malignancy. The number of suspicious sonographic features obtained with receiver operating characteristic analysis to discriminate between malignant and benign disease was three. Conclusion Sonographic scoring of thyroid nodules is an effective method for predicting malignancy. The authors suggest including associated pathologic node in the scoring criteria. Further studies with larger cohorts

  20. Nitrogen control of bacterial signal production in Rhizobium meliloti-alfalfa symbiosis.

    Science.gov (United States)

    Dusha, Ilona

    2002-09-01

    Under nitrogen-depleted conditions nitrogen-fixing soil bacteria of the family Rhizobiaceae are able to induce symbiotic nodules on the roots of leguminous plants where bacteroids convert atmospheric nitrogen to ammonia. The presence of exogenous nitrogen source inhibits the development and the functioning of bacterium-plant symbiosis. Earlier experiments demonstrated that nitrate inhibited all stages of symbiotic interaction, affecting primarily the host functions. The investigation of the possible involvement of the microsymbiont in nitrogen regulation showed that two signalling steps were controlled by ammonium. The synthesis of the first bacterial signal, the Nod factor was repressed by ammonium. The nitrogen signal is conveyed to nodulation (nod) genes by the general nitrogen regulatory (ntr) system and by the nodD3-syrM self-amplifying system. The fine control also involves a negative regulatory factor, ntrR. When ntrR is mutated, more efficient nodule formation and nitrogen fixation is observed in symbiosis with alfalfa even in the presence of ammonium. The biosynthesis of the second bacterial signal succinoglycan is also controlled by ammonium. SyrM, a common regulatory factor for nod and exo gene expression, may contribute to the adjustment of the amount of succinoglycan and the ratio of its biologically active form.

  1. Blue light does not inhibit nodulation in Sesbania rostrata.

    Science.gov (United States)

    Shimomura, Aya; Arima, Susumu; Hayashi, Makoto; Maymon, Maskit; Hirsch, Ann M; Suzuki, Akihiro

    2017-01-02

    Earlier, we reported that root nodulation was inhibited by blue light irradiation of Lotus japonicus. Because some legumes do not establish nodules exclusively on underground roots, we investigated whether nodule formation in Sesbania rostrata, which forms both root and "stem" nodules following inoculation with Azorhizobium caulinodans, is inhibited by blue light as are L. japonicus nodules. We found that neither S. rostrata nodulation nor nitrogen fixation was inhibited by blue light exposure. Moreover, although A. caulinodans proliferation was not affected by blue light irradiation, bacterial survival was decreased. Therefore, blue light appears to impose different responses depending on the legume-rhizobial symbiosis.

  2. Crowdsourcing the nodulation gene network discovery environment.

    Science.gov (United States)

    Li, Yupeng; Jackson, Scott A

    2016-05-26

    The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing symbiotic microbes. With the aim of understanding the underlying molecular mechanisms leading to nodulation, many efforts are underway to identify nodulation-related genes and determine how these genes interact with each other. In order to accurately and efficiently reconstruct nodulation gene network, a crowdsourcing platform, CrowdNodNet, was created. The platform implements the jQuery and vis.js JavaScript libraries, so that users are able to interactively visualize and edit the gene network, and easily access the information about the network, e.g. gene lists, gene interactions and gene functional annotations. In addition, all the gene information is written on MediaWiki pages, enabling users to edit and contribute to the network curation. Utilizing the continuously updated, collaboratively written, and community-reviewed Wikipedia model, the platform could, in a short time, become a comprehensive knowledge base of nodulation-related pathways. The platform could also be used for other biological processes, and thus has great potential for integrating and advancing our understanding of the functional genomics and systems biology of any process for any species. The platform is available at http://crowd.bioops.info/ , and the source code can be openly accessed at https://github.com/bioops/crowdnodnet under MIT License.

  3. Eficiência de inoculantes de rizóbio na nodulação de alfafa em solo de cerrado Efficiency of rhizobia inoculants on nodulation of alfalfa in a "cerrado" soil

    Directory of Open Access Journals (Sweden)

    Deise Ferreira Xavier

    2005-06-01

    harvest was performed at 5 cm height from ground level, to determine dry matter (DM weight and total-N in the above ground parts. At ninety days, the whole plants were sampled, to measure the DM yield of both above ground parts and roots, and N content of above ground parts. The presence of nodules in the roots was examined. Results of DM yield of above ground parts and roots, and of total-N in the above ground parts, indicated that the two commercial inoculants used were efficient for all the three alfalfa cultivars in the soil, which had its pH corrected. Regarding nodulation, the checks with and without nitrogen did not nodulate, indicating that Rhizobium meliloti was not present in the soil. These observations reinforce the need of inoculation of alfalfa with appropriate rhizobia in tropical regions.

  4. [Cytogenic chorionic nodule of the uterus].

    Science.gov (United States)

    Frappart, L; Lin, H C; Gauthier, A M; Griot, A; Palayer, C; Vernevaut, Y; Bremond, A; Rochet, Y; Lesbros, F

    1985-01-01

    The authors report five observations of endometrial stromal nodules. These nodules are composed of cells identical to those of the endometrial stroma. They constitute the benign form of endometrial stromal tumors. From the macroscopic point of view, they present as nodular formations, most often single, well defined, non-fasciculated, whitish or yellowish sometimes cystisized. From the microscopic point of view, these nodules contain areas of plexiform or glandular arrangement with, occasionally, pseudo-rosettes. Small collagenous zones can often be observed. E.S.N. should be distinguished on the one hand from endolymphatic stromal myosis, and on the other hand from sarcoma of the endometrial stroma. Histogenesis of the lesion is also discussed.

  5. Deep-ocean ferromanganese crusts and nodules

    Science.gov (United States)

    Hein, James R.; Koschinsky, Andrea

    2014-01-01

    Ferromanganese crusts and nodules may provide a future resource for a large variety of metals, including many that are essential for emerging high- and green-technology applications. A brief review of nodules and crusts provides a setting for a discussion on the latest (past 10 years) research related to the geochemistry of sequestration of metals from seawater. Special attention is given to cobalt, nickel, titanium, rare earth elements and yttrium, bismuth, platinum, tungsten, tantalum, hafnium, tellurium, molybdenum, niobium, zirconium, and lithium. Sequestration from seawater by sorption, surface oxidation, substitution, and precipitation of discrete phases is discussed. Mechanisms of metal enrichment reflect modes of formation of the crusts and nodules, such as hydrogenetic (from seawater), diagenetic (from porewaters), and mixed diagenetic–hydrogenetic processes.

  6. Seabed topography and distribution of manganese nodules in the Central Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Pattan, J.N.; Kodagali, V.N.

    The relationship between seabed topography and distribution of nodules, recovery of free fall grab samplers, nodule size and chemical composition of manganese nodules in the Central Indian Ocean have been studied. Nodule abundance was greater (4...

  7. Lung Nodule Detection via Deep Reinforcement Learning

    Directory of Open Access Journals (Sweden)

    Issa Ali

    2018-04-01

    Full Text Available Lung cancer is the most common cause of cancer-related death globally. As a preventive measure, the United States Preventive Services Task Force (USPSTF recommends annual screening of high risk individuals with low-dose computed tomography (CT. The resulting volume of CT scans from millions of people will pose a significant challenge for radiologists to interpret. To fill this gap, computer-aided detection (CAD algorithms may prove to be the most promising solution. A crucial first step in the analysis of lung cancer screening results using CAD is the detection of pulmonary nodules, which may represent early-stage lung cancer. The objective of this work is to develop and validate a reinforcement learning model based on deep artificial neural networks for early detection of lung nodules in thoracic CT images. Inspired by the AlphaGo system, our deep learning algorithm takes a raw CT image as input and views it as a collection of states, and output a classification of whether a nodule is present or not. The dataset used to train our model is the LIDC/IDRI database hosted by the lung nodule analysis (LUNA challenge. In total, there are 888 CT scans with annotations based on agreement from at least three out of four radiologists. As a result, there are 590 individuals having one or more nodules, and 298 having none. Our training results yielded an overall accuracy of 99.1% [sensitivity 99.2%, specificity 99.1%, positive predictive value (PPV 99.1%, negative predictive value (NPV 99.2%]. In our test, the results yielded an overall accuracy of 64.4% (sensitivity 58.9%, specificity 55.3%, PPV 54.2%, and NPV 60.0%. These early results show promise in solving the major issue of false positives in CT screening of lung nodules, and may help to save unnecessary follow-up tests and expenditures.

  8. Large philipsite crystal as ferromanganese nodule nucleus

    Digital Repository Service at National Institute of Oceanography (India)

    Ghosh, A.K.; Mukhopadhyay, R.

    absorption spectophotometry. Samples for AAS analysis were prepared using standard HF, HNO3, HC103, and HCI treatment and analyzed with 0.1 N HCI solution, along with a USGS A1 manganese nodule standard. The precision of the analyses was better than ~ 5~o... of ferroxyhydroxides in siliceous sediments (profle N3, Fig. 2), thus leaving free Mn to form todorokite-rich nodules (Nath and Rao 1988). Todorokite effectively incorporates Cu and Ni in their crystal struc- ture, and an increase in the concentration...

  9. Proteome reference maps of the Lotus japonicus nodule and root

    DEFF Research Database (Denmark)

    Dam, Svend Secher; Dyrlund, Thomas F.; Ussatjuk, Anna

    2014-01-01

    stress level at this developmental stage. In contrast, protein spots corresponding to nodulins such as leghemoglobin, asparagine synthetase, sucrose synthase, and glutamine synthetase were prevalent in red nodules. The distinct biochemical state of nodules was further highlighted by the conspicuous...

  10. Grade distributions in manganese nodules of Central Indian Ocean Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Sudhakar, M.

    Data concerning to geological setting physical characteristics and bulk chemical composition of the nodules sampled from CIOB were stored in the Computer Data Bank of this Institute. Bulk chemical composition of nodules, in which grade is expressed...

  11. Solitary necrotic nodule of the liver: parasitic origin?

    OpenAIRE

    Tsui, W. M.; Yuen, R. W.; Chow, L. T.; Tse, C. C.

    1992-01-01

    AIMS: To report further cases of solitary necrotic nodule of the liver and to study its nature. METHODS: Seven nodules were retrieved from 4000 necropsy and surgical liver specimens coming to light over the past five years. All of them satisfied the diagnostic criteria of solitary necrotic nodule: a solid lesion with a central necrotic core and a hyalinised fibrotic capsule containing elastic fibres. Their clinicopathological features were reviewed. RESULTS: The nodules were incidental findin...

  12. Buried nodules from the central Indian Ocean basin

    Digital Repository Service at National Institute of Oceanography (India)

    Pattan, J.N.; Parthiban, G.

    m. Maximum of 15 buried nodules were recovered in one core (AAS-22/ GC-07) and maximum depth where buried nodule recovered is at 5.35 m depth below seafloor. In the present study a total of twenty buried nodules from four sediment cores were utilized...

  13. Effectiveness of native Rhizobium on nodulation and growth ...

    African Journals Online (AJOL)

    This study was conducted in order to evaluate the symbiotic effectiveness of native Rhizobium isolated strains on number of nodule, weight, and morphological properties of dry bean. To realize this purpose, fresh and healthy root nodules were collected from major dry bean-growing districts of Konya, Turkey. These nodules ...

  14. Root nodule organogenesis : molecular characterization of the zonation central tissue

    NARCIS (Netherlands)

    Yang, W.C.

    1994-01-01

    Legume plants form root nodules by interacting with the soil bacterium, Rhizobium. In these nodules bacteria are able to convert atmospheric nitrogen into ammonia which is used by the host plants as nitrogen source. Therefore symbiotic nitrogen fixation in root nodules

  15. Compact-Morphology-based poly-metallic Nodule Delineation.

    Science.gov (United States)

    Schoening, Timm; Jones, Daniel O B; Greinert, Jens

    2017-10-17

    Poly-metallic nodules are a marine resource considered for deep sea mining. Assessing nodule abundance is of interest for mining companies and to monitor potential environmental impact. Optical seafloor imaging allows quantifying poly-metallic nodule abundance at spatial scales from centimetres to square kilometres. Towed cameras and diving robots acquire high-resolution imagery that allow detecting individual nodules and measure their sizes. Spatial abundance statistics can be computed from these size measurements, providing e.g. seafloor coverage in percent and the nodule size distribution. Detecting nodules requires segmentation of nodule pixels from pixels showing sediment background. Semi-supervised pattern recognition has been proposed to automate this task. Existing nodule segmentation algorithms employ machine learning that trains a classifier to segment the nodules in a high-dimensional feature space. Here, a rapid nodule segmentation algorithm is presented. It omits computation-intense feature-based classification and employs image processing only. It exploits a nodule compactness heuristic to delineate individual nodules. Complex machine learning methods are avoided to keep the algorithm simple and fast. The algorithm has successfully been applied to different image datasets. These data sets were acquired by different cameras, camera platforms and in varying illumination conditions. Their successful analysis shows the broad applicability of the proposed method.

  16. Geochemistry of polymetallic nodules from the Central Indian Ocean basin

    Digital Repository Service at National Institute of Oceanography (India)

    Valsangkar, A; Khadge, N.H.; Desa, J.A

    the thirteen different types of nodules present, only spherical and ellipsoidal nodules ranging in size from 2 cm to 2-4 cm with a rough, granular texture are abundant in the siliceous sediments. Different-sized nodules from the CIOB suggest formation...

  17. Host range, symbiotic effectiveness and nodulation competitiveness ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... This symbiotic interaction is of agronomic and ecological importance because of its significant amount of nitrogen to the total nitrogen budget in terrestrial ecosystems (Postgate,. 1998). An important characteristic of this symbiotic interaction is host specificity, where defined species of rhizobia forms nodules ...

  18. Vocal fold nodules: morphological and immunohistochemical investigations.

    Science.gov (United States)

    Martins, Regina Helena Garcia; Defaveri, Julio; Custódio Domingues, Maria Aparecida; de Albuquerque E Silva, Rafael; Fabro, Alexandre

    2010-09-01

    The objective of this study was to investigate the morphological and immunohistochemical characteristics of vocal fold nodules. The study design was prospective and retrospective. For the histological study, we reviewed 15 slides from the surgical cases of vocal fold nodules, in which we analyzed epithelium, basal membrane (bm), and lamina propria. For the transmission and scanning electron microscopy (TEM, SEM) studies, five new cases on vocal fold nodules were included. Immunohistochemistry study was carried out in the 15 specimens, using antifibronectin, antilaminin, and anticollagen IV antibodies. The main histological alterations were epithelial hyperplasia (73.33%), basement membrane thickening (86.66%), edema, and fibrosis (93.33%). SEM--reduction in mucous lacing and increase in the desquamating cells, without epithelial erosion. TEM--hyperplasia of the epithelium, enlargement of the intercellular junctions, which was filled by fluid, subepithelial thickening of the lamina reticularis, and break points in the basal membrane. Immunohistochemistry--we identified greater immunoexpression of fibronectin on the basal membrane, on the lamina propria, and around the vessels. Antilaminin and anticollagen IV antibodies showed higher pigmentation on the endothelium of the vessels than that on the basal membrane. In vocal fold nodules, combined assessment using light microscopy, electron microscopy, and immunohistochemistry can reveal important morphological details useful in characterizing these lesions. 2010 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  19. Les nodules thyroidiens: Aspects epidemiologiques, cliniques et ...

    African Journals Online (AJOL)

    Thyroidectomy practised in all the patients has been dominated by a unilateral lobo-isthmectomia (55.96%). Immediate post-operative effect have been simples in 94.05% of cases and complicated in 5.95% of cases. Thyroid nodules are frequent in TOGO and affect in 90.46% of cases women. It is an ailment of the young ...

  20. The hyperfunctioning nodules of the thyroid

    International Nuclear Information System (INIS)

    Rosenthal, D.

    1975-01-01

    Iodine kinetic studies, using a double label ( 131 I - and T 4 -125 I), were performed on 8 patients with hot thyroid nodules, 3 diffuse toxic goiters and one normal control. This investigation was complemented by partial kinetic studies done on 62 other subjetcs, including normal controls and euthyroid or hyperthyroid patients with diffuse or nodular goiter [pt

  1. A histochemical study of root nodule development

    NARCIS (Netherlands)

    Wiel, van de C.

    1991-01-01

    In cooperation with soil bacteria of the genera Rhizobium , Bradyrhizobium or Azorhizobium , many members of the legume family are able to form specialized organs on their roots, called root nodules. The bacteria, wrapped up

  2. Histoplasmosis presenting with solitary pulmonary nodule: Two ...

    African Journals Online (AJOL)

    Pulmonary histoplasmosis is a granulomatous disease, whose diagnosis is not always easy, as it may simulate metastatic lesions due to similar radiographic findings. We herein report two cases of histoplasmosis with solitary pulmonary nodule in asymptomatic patients with histories of cancer surgeries, whose diagnoses ...

  3. Histoplasmosis presenting with solitary pulmonary nodule: Two ...

    African Journals Online (AJOL)

    2014-08-04

    Aug 4, 2014 ... hospital because of a right pulmonary nodule, discovered on a follow‑up chest radiogram. He had a history of abdominoperineal resection for rectal ... Given the patient's history of tumor resection, the ... Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.

  4. US Diagnosis for Thyroid Nodules with an Indeterminate Cytology

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Jong Geun; Kim, Dong Wook [Busan Paik Hospital, Inje University College of Medicine, Busan (Korea, Republic of); Kang, Tae Woo [Saegyaero Hospital, Busan (Korea, Republic of)

    2011-09-15

    We wanted to assess the diagnostic efficacy of thyroid ultrasound (US) for evaluating thyroid nodules with indeterminate cytology. Among 1865 nodules in 1278 patients who received a prospective US diagnosis of their thyroid nodule(s) and who subsequently underwent US-guided fine-needle aspiration, 130 nodules with indeterminate cytology were enrolled in the study. Each thyroid nodule was prospectively classified by a single radiologist into 1 of 5 diagnostic categories: 'benign', 'probably benign', 'indeterminate', 'suspicious for malignancy' and 'malignant.' The solid nodules were classified using all 5 categories and the partially cystic nodules classified using 4 categories ('indeterminate' was omitted). We calculated the diagnostic efficacy of thyroid US by comparing the US diagnoses with the pathology results. Of 130 nodules with indeterminate cytology (130/1865, 7.0%), 62 nodules were surgically removed. Nineteen nodules were assigned to the indeterminate category on US. The malignantly rate of the US-indeterminate category was 56.5% (35/62). The sensitivity, specificity and positive and negative predictive values were 81.0%, 81.8%, 81.0%, 81.8% and 81.4%, respectively, when US-indeterminate nodules were excluded. There was no significant difference of diagnostic efficacy when these nodules were reclassified as malignant, but there was a significant difference of diagnostic efficacy when these nodules were reclassified as benign. Our US classification may be a feasible method for managing thyroid nodules with indeterminate cytology

  5. Giant hepatic regenerative nodules in Alagille syndrome

    International Nuclear Information System (INIS)

    Rapp, Jordan B.; Bellah, Richard D.; Anupindi, Sudha A.; Maya, Carolina; Pawel, Bruce R.

    2017-01-01

    Children with Alagille syndrome undergo surveillance radiologic examinations as they are at risk for developing cirrhosis and hepatocellular carcinoma. There is limited literature on the imaging of liver masses in Alagille syndrome. We report the ultrasound (US) and magnetic resonance imaging (MRI) appearances of incidental benign giant hepatic regenerative nodules in this population. To describe the imaging findings of giant regenerative nodules in patients with Alagille syndrome. A retrospective search of the hospital database was performed to find all cases of hepatic masses in patients with Alagille syndrome during a 10-year period. Imaging, clinical charts, laboratory data and available pathology were reviewed and analyzed and summarized for each patient. Twenty of 45 patients with confirmed Alagille syndrome had imaging studies. Of those, we identified six with giant focal liver masses. All six patients had large central hepatic masses that were remarkably similar on US and MRI, in addition to having features of cirrhosis. In each case, the mass was located in hepatic segment VIII and imaging showed the mass splaying the main portal venous branches at the hepatic hilum, as well as smaller portal and hepatic venous branches coursing through them. On MRI, signal intensity of the mass was isointense to liver on T1-weighted sequences in four of six patients, but hyperintense on T1 in two of six patients. In all six cases, the mass was hypointense on T2- weighted sequences. The mass post-contrast was isointense to adjacent liver in all phases in five the cases. Five out of six patients had pathological correlation demonstrating preserved ductal architecture confirming the final diagnosis of a regenerative nodule. Giant hepatic regenerative nodules with characteristic US and MR features can occur in patients with Alagille syndrome with underlying cirrhosis. Recognizing these lesions as benign giant hepatic regenerative nodules should, thereby, mitigate any need for

  6. Giant hepatic regenerative nodules in Alagille syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Rapp, Jordan B. [Lewis Katz School of Medicine at Temple University, Department of Radiology, Temple University Hospital, Philadelphia, PA (United States); Bellah, Richard D.; Anupindi, Sudha A. [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA (United States); Maya, Carolina [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); Pawel, Bruce R. [University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA (United States); The Children' s Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, Philadelphia, PA (United States)

    2017-02-15

    Children with Alagille syndrome undergo surveillance radiologic examinations as they are at risk for developing cirrhosis and hepatocellular carcinoma. There is limited literature on the imaging of liver masses in Alagille syndrome. We report the ultrasound (US) and magnetic resonance imaging (MRI) appearances of incidental benign giant hepatic regenerative nodules in this population. To describe the imaging findings of giant regenerative nodules in patients with Alagille syndrome. A retrospective search of the hospital database was performed to find all cases of hepatic masses in patients with Alagille syndrome during a 10-year period. Imaging, clinical charts, laboratory data and available pathology were reviewed and analyzed and summarized for each patient. Twenty of 45 patients with confirmed Alagille syndrome had imaging studies. Of those, we identified six with giant focal liver masses. All six patients had large central hepatic masses that were remarkably similar on US and MRI, in addition to having features of cirrhosis. In each case, the mass was located in hepatic segment VIII and imaging showed the mass splaying the main portal venous branches at the hepatic hilum, as well as smaller portal and hepatic venous branches coursing through them. On MRI, signal intensity of the mass was isointense to liver on T1-weighted sequences in four of six patients, but hyperintense on T1 in two of six patients. In all six cases, the mass was hypointense on T2- weighted sequences. The mass post-contrast was isointense to adjacent liver in all phases in five the cases. Five out of six patients had pathological correlation demonstrating preserved ductal architecture confirming the final diagnosis of a regenerative nodule. Giant hepatic regenerative nodules with characteristic US and MR features can occur in patients with Alagille syndrome with underlying cirrhosis. Recognizing these lesions as benign giant hepatic regenerative nodules should, thereby, mitigate any need for

  7. Determination of the chemical structure of the capsular polysaccharide of strain B33, a fast-growing soya bean-nodulating bacterium isolated from an arid region of China.

    Science.gov (United States)

    Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Ruiz-Sainz, J E; Buendía-Clavería, A M; Ollero, F J; Yang, S S; Gil-Serrano, A M

    2001-01-01

    We have determined the structure of a polysaccharide from strain B33, a fast-growing bacterium that forms nitrogen-fixing nodules with Asiatic and American soya bean cultivars. On the basis of monosaccharide analysis, methylation analysis, one-dimensional 1H- and 13C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a polymer having the repeating unit -->6)-4-O-methyl-alpha-D-Glcp-(1-->4)-3-O-methyl-beta-D-GlcpA-(1--> (where GlcpA is glucopyranuronic acid and Glcp is glucopyranose). Strain B33 produces a K-antigen polysaccharide repeating unit that does not have the structural motif sugar-Kdx [where Kdx is 3-deoxy-D-manno-2-octulosonic acid (Kdo) or a Kdo-related acid] proposed for different Sinorhizobium fredii strains, all of them being effective with Asiatic soya bean cultivars but unable to form nitrogen-fixing nodules with American soya bean cultivars. Instead, it resembles the K-antigen of S. fredii strain HH303 (rhamnose, galacturonic acid)n, which is also effective with both groups of soya bean cultivars. Only the capsular polysaccharide from strains B33 and HH303 have monosaccharide components that are also present in the surface polysaccharide of Bradyrhizobium elkanii strains, which consists of a 4-O-methyl-D-glucurono-L-rhamnan. PMID:11439101

  8. Uranium in Pacific deep-sea sediments and manganese nodules

    International Nuclear Information System (INIS)

    Kunzendorf, H.; Plueger, W.L.; Friedrich, G.H.

    1983-01-01

    A total of 1344 manganese nodules and 187 pelagic sediments from 9 areas in the North and the South Pacific were analyzed for U by the delayed-neutron counting technique. A strong positive correlation between U and Fe in nodules and sediments suggests a co-precipitative removal from sea water into the Fe-rich (ferromanganese mineral phase MnO 2 . Enrichment of U and Fe in nodules from the northwestern slopes of two submarine hills (U between 6 and 9 ppm) in the equatorial nodule belt is thought to be caused by directional bottom water flow creating elevated oxygenized conditions in areas opposed to the flow. Economically important nodule deposits from the nodule belt and the Peru Basin have generally low U contents, between 3 and 5 ppm. Insignificant resources of U of about 4 x 10 5 in the Pacific manganese nodules are estimated. (orig.)

  9. Dual energy computed tomography of lung nodules: Differentiation of iodine and calcium in artificial pulmonary nodules in vitro

    International Nuclear Information System (INIS)

    Knöß, Naomi; Hoffmann, Beata; Krauss, Bernhard; Heller, Martin; Biederer, Jürgen

    2011-01-01

    Background: Iodine enhancement is a marker for malignancy in pulmonary nodules. The purpose of this in vitro study was to assess whether dual energy computed tomography (DECT) can be used to detect iodine and to distinguish iodine from disperse calcifications in artificial pulmonary nodules. Materials and methods: Small, medium, and large artificial nodules (n = 54), with increasing concentrations of iodine or calcium corresponding to an increase in Hounsfield Units (HU) of 15, 30, 45, and 90 at 120 kV, were scanned in a chest phantom with DECT at 80 and 140 kV. Attenuation values of each nodule were measured using semi-automated volumetric analysis. The mean DE ratio with 95% confidence intervals (CI) was calculated for each nodule. Results: The mean maximum diameter of the 18 small nodules was 12 mm (standard deviation: 0.4), 16 mm (0.4) for the 18 medium nodules, and 30 mm (1.1) for the 18 large nodules. There was no overlap of 95% CI of DE ratios of iodine and calcium in nodules ≥16 mm. In nodules <16 mm, there was an overlap of DE ratios in low contrast lesions. Conclusion: DECT can distinguish iodine from calcium in artificial nodules ≥16 mm in vitro. In smaller lesions, a clear differentiation is not possible.

  10. New development of MR imaging lung nodule simulator for detecting peripheral pulmonary nodules: Experimental and clinical studies

    International Nuclear Information System (INIS)

    Kono, M.; Yamasaki, K.; Adachi, S.; Kameda, K.; Tanaka, K.

    1987-01-01

    There are no appropriate phantoms for MR imaging because the parameters (rho, T1, T2) are not equivalent to those in human tissues. To evaluate the detectability of peripheral lung nodules with MR imaging, the authors devised lung nodule phantoms made of polyvinyl alcohol for evaluating spatial and contrast resolution. To evaluate the environmental effect around the phantoms, a thoracic phantom was made of polyvinyl alcohol, solid oils and artificial bone. Based on experimental results, T1, T2 values of the lung nodule phantom varied as a function of position. To determine tissue characterization of peripheral lung nodules with MR imaging, lung nodule phantoms with T1 and T2 values similar to those of lung cancer were compared with actual T1 and T2 values of lung nodules. It was strongly suggested that these phantoms would be useful for differentiation of malignant nodules from inflammatory lesion

  11. Activation of cell divisions in legume nodulation

    DEFF Research Database (Denmark)

    Nadzieja, Marcin

    Leguminous plants engage into symbiotic relationships with soil bacteria, rhizobia, and develop root nodules. This process initiates with recognition of bacteria derived signalling molecules called nod factors. The subsequent events lead to symbiotic infection and, occurring in parallel, de novo...... was shown to require auxin signalling. Cytokinin, in contrast, exert a negative regulation of bacterial entry into the root. During organogenesis, auxin and cytokinin maxima are known to accompany nodule primordia development and together regulate progression through the cell cycle. Moreover, application...... the two hormones require further investigation. In order to improve understanding in these areas we aimed to develop and characterise hormone and cell division markers in Lotus japonicus. Using the extensive genetic resources available in L. japonicus, these markers may then be used to develop a more...

  12. Pulmonary nodule registration in serial CT scans based on rib anatomy and nodule template matching

    International Nuclear Information System (INIS)

    Shi Jiazheng; Sahiner, Berkman; Chan, H.-P.; Hadjiiski, Lubomir; Zhou, C.; Cascade, Philip N.; Bogot, Naama; Kazerooni, Ella A.; Wu, Y.-T.; Wei, J.

    2007-01-01

    An automated method is being developed in order to identify corresponding nodules in serial thoracic CT scans for interval change analysis. The method uses the rib centerlines as the reference for initial nodule registration. A spatially adaptive rib segmentation method first locates the regions where the ribs join the spine, which define the starting locations for rib tracking. Each rib is tracked and locally segmented by expectation-maximization. The ribs are automatically labeled, and the centerlines are estimated using skeletonization. For a given nodule in the source scan, the closest three ribs are identified. A three-dimensional (3D) rigid affine transformation guided by simplex optimization aligns the centerlines of each of the three rib pairs in the source and target CT volumes. Automatically defined control points along the centerlines of the three ribs in the source scan and the registered ribs in the target scan are used to guide an initial registration using a second 3D rigid affine transformation. A search volume of interest (VOI) is then located in the target scan. Nodule candidate locations within the search VOI are identified as regions with high Hessian responses. The initial registration is refined by searching for the maximum cross-correlation between the nodule template from the source scan and the candidate locations. The method was evaluated on 48 CT scans from 20 patients. Experienced radiologists identified 101 pairs of corresponding nodules. Three metrics were used for performance evaluation. The first metric was the Euclidean distance between the nodule centers identified by the radiologist and the computer registration, the second metric was a volume overlap measure between the nodule VOIs identified by the radiologist and the computer registration, and the third metric was the hit rate, which measures the fraction of nodules whose centroid computed by the computer registration in the target scan falls within the VOI identified by the

  13. Interstitial laser photocoagulation for benign thyroid nodules: time to treat large nodules.

    Science.gov (United States)

    Amabile, Gerardo; Rotondi, Mario; Pirali, Barbara; Dionisio, Rosa; Agozzino, Lucio; Lanza, Michele; Buonanno, Luciano; Di Filippo, Bruno; Fonte, Rodolfo; Chiovato, Luca

    2011-09-01

    Interstitial laser photocoagulation (ILP) is a new therapeutic option for the ablation of non-functioning and hyper-functioning benign thyroid nodules. Amelioration of the ablation procedure currently allows treating large nodules. Aim of this study was to evaluate the therapeutic efficacy of ILP, performed according to a modified protocol of ablation, in patients with large functioning and non-functioning thyroid nodules and to identify the best parameters for predicting successful outcome in hyperthyroid patients. Fifty-one patients with non-functioning thyroid nodules (group 1) and 26 patients with hyperfunctioning thyroid nodules (group 2) were enrolled. All patients had a nodular volume ≥40 ml. Patients were addressed to 1-3 cycles of ILP. A cycle consisted of three ILP sessions, each lasting 5-10 minutes repeated at an interval of 1 month. After each cycle of ILP patients underwent thyroid evaluation. A nodule volume reduction, expressed as percentage of the basal volume, significantly occurred in both groups (F = 190.4; P < 0.0001 for group 1 and F = 100.2; P < 0.0001 for group 2). Receiver-operator-characteristic (ROC) curves were constructed for: (i) percentage of volume reduction; (ii) difference in nodule volume; (iii) total amount of energy delivered expressed in Joule. ROC curves identified the percentage of volume reduction as the best parameter predicting a normalized serum TSH (area under the curve 0.962; P < 0.0001). Intraoperative complications consisted in: (i) mild pain occurring in five (6.5%) patients, (ii) vasovagal reaction in two (2.6%) patients, (iii) fever within 24 hours from ILP in five (6.5%) patients. No major complications including persistent pain, laringeal nerve dysfunction, hypoparathyroidism, pseudocystic transformation, and/or neck fascitis were observed. ILP represents a valid alternative to surgery also for large benign thyroid nodules, both in terms of nodule size reduction and cure of

  14. Segmentation of nodules on chest computed tomography for growth assessment

    International Nuclear Information System (INIS)

    Mullally, William; Betke, Margrit; Wang Jingbin; Ko, Jane P.

    2004-01-01

    Several segmentation methods to evaluate growth of small isolated pulmonary nodules on chest computed tomography (CT) are presented. The segmentation methods are based on adaptively thresholding attenuation levels and use measures of nodule shape. The segmentation methods were first tested on a realistic chest phantom to evaluate their performance with respect to specific nodule characteristics. The segmentation methods were also tested on sequential CT scans of patients. The methods' estimation of nodule growth were compared to the volume change calculated by a chest radiologist. The best method segmented nodules on average 43% smaller or larger than the actual nodule when errors were computed across all nodule variations on the phantom. Some methods achieved smaller errors when examined with respect to certain nodule properties. In particular, on the phantom individual methods segmented solid nodules to within 23% of their actual size and nodules with 60.7 mm3 volumes to within 14%. On the clinical data, none of the methods examined showed a statistically significant difference in growth estimation from the radiologist

  15. Pemphigus Vulgaris with Solitary Toxic Thyroid Nodule

    Directory of Open Access Journals (Sweden)

    Mostafa Alfishawy

    2014-01-01

    Full Text Available Background. Pemphigus vulgaris is an autoimmune vesiculobullous disease, affecting the skin and mucous membranes. It is reported to be associated with other autoimmune diseases including autoimmune thyroid diseases. However we report herein a case of pemphigus vulgaris associated with autonomous toxic nodule. Case Presentation. A 51-year-old woman was evaluated for blisters and erosions that develop on her trunk, face, and extremities, with a five-year history of progressively enlarging neck mass, and a past medical history of pemphigus vulgaris seven years ago. The condition was associated with palpitation, dyspnea, and heat intolerance. Thyroid function tests and thyroid scan were compatible with the diagnosis of thyrotoxicosis due to autonomous toxic nodule. Exacerbation of pemphigus vulgaris was proved by skin biopsy from the patient which revealed histologic picture of pemphigus vulgaris. Conclusion. Autoimmune thyroid diseases are reported to associate pemphigus vulgaris. To our knowledge, this case is the first in the English literature to report association between pemphigus vulgaris and autonomous toxic nodule and highlights the possibility of occurrence of pemphigus vulgaris with a nonautoimmune thyroid disease raising the question: is it just a coincidence or is there an explanation for the occurrence of both conditions together?

  16. Nitrogen assimilation in soybean nodules, 2

    International Nuclear Information System (INIS)

    Ohyama, Takuji; Kumazawa, Kikuo

    1980-01-01

    15 N assimilation was studied in bacteroid and cytosol fractions of soybean nodules. In the first experiment, after exposing the intact nodules to 15 N 2 for 5 min and 10 min, most of the fixed 15 N was detected in cytosol fraction. In cytosol fraction, 15 N content of glutamine was the highest and followed by glutamic acid, alanine, and allantoin in this sequence, whereas, in bacteroid fraction, glutamic acid showed the highest 15 N content and alanine and glutamine followed. In the second experiment, 15 N assimilation of various 15 N-labeled compounds in the separated bacteroid and cytosol fractions was investigated. In the separated bacteroid fraction which was fed with 15 NH 4 , 15 N was incorporated very rapidly into glutamic acid, alanine, and aspartic acid, but very slowly into glutamine. From these results, it was suggested that most of the fixed ammonia was exported to cytosol and assimilated via glutamine synthetase to glutamine, then via glutamate synthase to glutamic acid, and from these compounds various nitrogenous compounds were formed, but in bacteroids glutamate dehydrogenase and alanine dehydrogenase played an important role in the assimilation of fixed ammonia though quantitatively the contribution to ammonia assimilation in nodules was much less compared with cytosol. (author)

  17. Co-inoculation of arbusculr mycorrhizae and nitrogen fixing bacteria enhance alfalfa yield under saline conditions

    International Nuclear Information System (INIS)

    Zhu, R.; Tang, F.; Liu, F.; Chen, J.

    2016-01-01

    The study was to investigate the effects of combined inoculation of Glomus mosseae (arbusculr mycorrhizae fungi, AMF) and Sinorhizobium meliloti (nitrogen-fixing bacteria, i.e., an Rhizobium meliloti, RM) on yield, nutrient contents, nodulation and mycorrhizal colonization of different alfalfa cultivars under saline conditions. An experiment was conducted to test the efficacy of AMF and RM inoculation in development of salt tolerance in alfalfa cultivars (Zhaodong, Nongjing and Longmu) under different salinity levels (0, 60, 120 and 180 mM NaCl). We found that under non stress condition, double inoculation of alfalfa with rhizobium and AM increased the alfalfa yield, nodule weight and number, as well as shoot proline contents, the most when plants were double inoculated followed by AM and rhizobium inoculation, respectively. Whereas under salinity condition, double inoculation of alfalfa with rhizobium and AM increased alfalfa yield, mycorrhizal infection, nodule weight and number as well as increased in shoot proline content, the most followed by AM and rhizobium inoculation, respectively. The Results suggest that growth of alfalfa may be improved by combined inoculation of alfalfa with AM and rhizobium under salt and non-stress conditions. Alleviation of alfalfa growth under saline condition was perhaps due to an increase in mycorrhizal infection and nodule weight and number as well as an increased in shoot proline content by dual inoculation. (author)

  18. CT SCAN EVALUATION OF PULMONARY NODULE

    Directory of Open Access Journals (Sweden)

    A. Ravi Kumar

    2016-06-01

    Full Text Available BACKGROUND Lung carcinomas are quite commonly diagnosed. Thanks to the ever increasing smokers’ population. Majority of the city dwellers are at a higher risk of having this disease when compared to the village counterparts. The stigma through which the person and the family have to undergo before confirming the diagnosis is enormous. So the radiographic methods of diagnosing the malignancies have to improve. Before confirming the diagnosis, the radiologists, the treating physicians should be somewhat confident about the diagnosis so as to prepare the patients and their relatives for the most probable diagnosis before the confirmatory report. The confirmatory procedures include the PET scan and the Histopathology. Both are time consuming procedures and in an economy like ours, finding a PET scanning centre is rather difficult. So the most probable diagnosis has to be thought of using minimal resource. This study puts in a sincere effort to understand and evaluate the pulmonary nodule when identified by a CT scan. This paper is intended to help the practicing radiologists and also make life easy for a practicing physician to identify correctly the lesions and also help the patients to prevent further progression of the disease. METHODS The study was a cross-sectional study. The sample size of the study consisted of thirty patients. CT scan was done in thirty patients who were identified to have lung nodules either by other mode of radiological studies or first time identified in a CT scan itself. The study was conducted in Fathima Institute of Medical Sciences, Kadapa. The study was conducted from 2014 to 2015. RESULT Non-solid nodules were more in number when compared to the solid nodules. All the non-solid nodules were confirmed to be adenomas. Eighty percent of the nodules which were more than 8 mm in size were confirmed to be malignant. One hundred percent of the spiculated border on CT was confirmed to be malignant. In the present study

  19. A thyroid nodule classification method based on TI-RADS

    Science.gov (United States)

    Wang, Hao; Yang, Yang; Peng, Bo; Chen, Qin

    2017-07-01

    Thyroid Imaging Reporting and Data System(TI-RADS) is a valuable tool for differentiating the benign and the malignant thyroid nodules. In clinic, doctors can determine the extent of being benign or malignant in terms of different classes by using TI-RADS. Classification represents the degree of malignancy of thyroid nodules. TI-RADS as a classification standard can be used to guide the ultrasonic doctor to examine thyroid nodules more accurately and reliably. In this paper, we aim to classify the thyroid nodules with the help of TI-RADS. To this end, four ultrasound signs, i.e., cystic and solid, echo pattern, boundary feature and calcification of thyroid nodules are extracted and converted into feature vectors. Then semi-supervised fuzzy C-means ensemble (SS-FCME) model is applied to obtain the classification results. The experimental results demonstrate that the proposed method can help doctors diagnose the thyroid nodules effectively.

  20. Small Nodules Localization on CT Images of Lungs

    Science.gov (United States)

    Snezhko, E. V.; Kharuzhyk, S. A.; Tuzikov, A. V.; Kovalev, V. A.

    2017-05-01

    According to the World Health Organization (WHO) lung cancer remains the leading cause of death of men among all malignant tumors [1, 2]. One of the reasons of such a statistics is the fact that the lung cancer is hardly diagnosed on the yearly stages when it is almost asymptomatic. The purpose of this paper is to present a Computer-Aided Diagnosis (CAD) software developed for assistance of early detection of nodules in CT lung images including solitary pulmonary nodules (SPN) as well as multiple nodules. The efficiency of nodule localization was intended to be as high as the level of the best practice. The software developed supports several functions including lungs segmentation, selection of nodule candidates and nodule candidates filtering.

  1. The Relation between Occupational Exposure and Thyroid Nodules, Isfahan 2008

    OpenAIRE

    Afshin Rezazadeh; Atoosa Adibi

    2010-01-01

    Background/Objective: Considering that thyroid nodules and thyroid cancer occur more frequently in people exposed chronically to radiation, the aim of this study was to evaluate the prevalence of thyroid nodules in a population occupationally exposed to radiation, in hospitals of Isfahan city."nPatients and Methods: In this case-control study, the prevalence of thyroid nodules in radiation exposed workers was determined by ultrasonography. The control group was selected from a community ...

  2. Evaluation of diffuse thyroid diseases and thyroid nodules by CT

    International Nuclear Information System (INIS)

    Okamoto, Kyoko; Imanishi, Yoshimasa; Nakaji, Shunsuke; Shinagawa, Toshihito

    2007-01-01

    Imanishi et al. have previously reported that the changes in CT values reveal not only the change in iodine concentration in thyroid follicles, but also represent secondary changes in follicular content and follicular cells and/or interstitial structures. Thus, we performed thyroid CT without contrast material in 138 controls, 417 cases with diffuse thyroid diseases, and 279 cases with thyroid nodules, and evaluated the CT images based on the relation between the change in CT values and pathological changes. In 89% of the controls and 43% of patients with diffuse thyroid diseases, the thyroid CT revealed diffuse high density. In contrast, the 94% of thyroids that demonstrated diffuse low density were from patients with diffuse thyroid diseases. Eighty-four percent of malignant nodules and 64% of benign nodules had inhomogeneous densities, and only 26% of benign thyroid nodules had homogeneous density. However, 71% of nodules that showed high and low densities with regular and clear borders, and 82% of nodules that showed papillary proliferation in a cyst pattern were benign. Although only 58% of nodules with calcification were malignant, 66% of nodules with calcification in the central portion, and 86% of nodules with calcification of a disseminated and convergent pattern in distribution were malignant. Sixty-two percent of thyroids that surrounded nodules had chronic thyroiditis, hypoplasia and/or adenomatous goiter. Thus, unclear borders between a nodule and the surrounding thyroid tissue did not increase the possibility of malignancy. However, the unclear and/or lobulated border between a nodule and extra thyroid tissue increased the possibility of malignancy. We concluded that thyroid CT without contrast material is useful for the diagnosis of thyroid diseases. (author)

  3. THE STUDY OF CLINICAL PRESENTATION OF SOLITARY NODULE THYROID

    Directory of Open Access Journals (Sweden)

    Lakshmikanthan Premalatha

    2017-07-01

    Full Text Available BACKGROUND Thyroid disorders are the most common endocrine disorder seen in clinical practice and solitary thyroid nodule is one of the common presentations of thyroid disease. A discrete swelling in an otherwise impalpable gland is termed isolated or solitary nodule of thyroid.1 The prevalence of thyroid nodule increases from near zero at 15 years to 50% by about 60 to 65 years on sonography. At most 10% of these nodules are palpable even by experienced clinicians. This study is about the clinical presentation, histopathology and management of solitary nodule thyroid in MGM GH Tiruchirappalli. AIMS AND OBJECTIVES- To determine the age and sex incidence among the cases of solitary nodule thyroid. To study the percentage of euthyroid, hypothyroid or hyperthyroid state in patients presenting with solitary nodule thyroid. To study the proportion of malignant and benign cases among the solitary nodule thyroid at M.G.M. Govt. Hospital, Tiruchirappalli. MATERIALS AND METHODS This study includes 58 cases of solitary nodule of thyroid noted during the period Jan 2016-Dec 2016. Factors were tabulated and analysed statistically. RESULTS From the present study, the mean age at presentation found to be 42.5 years with preponderance to females. Because of periods of fluctuations in the demands of the hormonal requirement in female in their life cycle (puberty, menstrual cycles, pregnancy, menopause, the chances of thyroid nodule formation are very high as compared with male counterparts. From the study, distribution of malignancy is about 10.34. The incidence of malignancy found to be 12%, sensitivity is 87.5%, specificity is 100% for FNAC and HPE. CONCLUSION Majority of the patients are between 30-49 years of age. Incidence of solitary thyroid nodule is more common in female. Female: male ratio is almost about 15:1 Commonest symptom is swelling over anterior or lateral aspect of neck Among the benign lesion dominant nodule is most common and papillary and

  4. Indian exploration for polymetallic nodules in the central Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    ShyamPrasad, M.

    depths between 4000 – 6000 metres, low rates of sedimentation, source supply of metals. Fig. 1. Various ocean basins in the Indian Ocean which show presence of manganese nodules. Of these, the Central Indian Ocean Basin has proved... demand and supply equations. One important parameter that one needs to consider is that there is no known nodule exploitation system developed on a commercial scale at the moment and also that all large nodule deposits are 57 beyond the EEZ...

  5. Multimodal imaging of choroidal nodules in neurofibromatosis type-1

    Directory of Open Access Journals (Sweden)

    Vinod Kumar

    2018-01-01

    Full Text Available Choroidal nodules in neurofibromatosis type-1 are common and are best imaged with near-infrared reflectance (NIR imaging. The authors describe swept-source optical coherence tomography angiography (SSOCTA of choroidal nodules. These nodules are seen as hyperflow areas on SSOCTA and correlate well to bright patches on NIR imaging. The utility of multicolor scanning laser imaging in detecting these abnormalities is also described.

  6. Subsolid pulmonary nodules: imaging evaluation and strategic management.

    Science.gov (United States)

    Godoy, Myrna C B; Sabloff, Bradley; Naidich, David P

    2012-07-01

    Given the higher rate of malignancy of subsolid pulmonary nodules and the considerably lower growth rate of ground-glass nodules (GGNs), dedicated standardized guidelines for management of these nodules have been proposed, including long-term low-dose computed tomography (CT) follow-up (≥3 years). Physicians must be familiar with the strategic management of subsolid pulmonary nodules, and should be able to identify imaging features that suggest invasive adenocarcinoma requiring a more aggressive management. Low-dose CT screening studies for early detection of lung cancer have increased our knowledge of pulmonary nodules, and in particular our understanding of the strong although imperfect correlation of the subsolid pulmonary nodules, including pure GGNs and part-solid nodules, with the spectrum of preinvasive to invasive lung adenocarcinoma. Serial CT imaging has shown stepwise progression in a subset of these nodules, characterized by increase in size and density of pure GGNs and development of a solid component, the latter usually indicating invasive adenocarcinoma. There is close correlation between the CT features of subsolid nodules (SSNs) and the spectrum of lung adenocarcinoma. Standardized guidelines are suggested for management of SSNs.

  7. Asymptomatic Papulo-nodules Localized to One Finger

    Science.gov (United States)

    Rambhia, Kinjal D; Khopkar, Uday S

    2015-01-01

    Subcutaneous or deep granuloma annulare is a benign asymptomatic condition characterized by firm asymptomatic nodules in deep subcutaneous tissues that may be associated with intradermal lesions. A 53-year-old female presented with asymptomatic skin-colored, firm nodules over the right ring finger. Histopathology revealed a palisading granuloma with central degenerated collagen and mucin deposition in the dermis suggestive of granuloma annulare. Isolated and unilateral involvement of a single digit with clusters of nodules of subcutaneous granuloma annulare (GA) in an adult is rare and differentiation from its simulator rheumatoid nodule is essential. PMID:26538728

  8. Hyper-functioning Thyroid Nodule with Scintigraphic Owl's Eye Appearance

    International Nuclear Information System (INIS)

    Al-Kordi, R.S.; Elgazzar, A.H.

    2006-01-01

    Hyper-functioning thyroid nodules may produce various scintigraphic appearances on thyroid scans. Autonomously hyper functioning thyroid nodules invariably demonstrate degenerative changes. These changes may give rise to central or less commonly peripheral photopenic areas on a thyroid scan within otherwise a hot nodule. In this report we present a case of hyper functioning autonomous nodule with peripheral degeneration and residual central functioning tissue giving the appearance of an owl's eye. Although rare, this pattern can be seen in a variety of benign and malignant thyroid conditions. (author)

  9. Automatic Solitary Lung Nodule Detection in Computed Tomography Images Slices

    Science.gov (United States)

    Sentana, I. W. B.; Jawas, N.; Asri, S. A.

    2018-01-01

    Lung nodule is an early indicator of some lung diseases, including lung cancer. In Computed Tomography (CT) based image, nodule is known as a shape that appears brighter than lung surrounding. This research aim to develop an application that automatically detect lung nodule in CT images. There are some steps in algorithm such as image acquisition and conversion, image binarization, lung segmentation, blob detection, and classification. Data acquisition is a step to taking image slice by slice from the original *.dicom format and then each image slices is converted into *.tif image format. Binarization that tailoring Otsu algorithm, than separated the background and foreground part of each image slices. After removing the background part, the next step is to segment part of the lung only so the nodule can localized easier. Once again Otsu algorithm is use to detect nodule blob in localized lung area. The final step is tailoring Support Vector Machine (SVM) to classify the nodule. The application has succeed detecting near round nodule with a certain threshold of size. Those detecting result shows drawback in part of thresholding size and shape of nodule that need to enhance in the next part of the research. The algorithm also cannot detect nodule that attached to wall and Lung Chanel, since it depend the searching only on colour differences.

  10. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales

    Science.gov (United States)

    The intracellular plant pathogen ‘Ca. Liberibacter asiaticus’ is a member of the Rhizobiales, as are the nitrogen fixing Sinorhizobium meliloti and Bradyrhizobium japonicum, the plant pathogen Agrobacterium tumefaciens and the intracellular mammalian pathogen Bartonella henselae. Whole genome compar...

  11. Comparison of the 'Ca Liberibacter asiaticus' genome adapted for an intracellular lifestyle with other members of the rhizobiales

    Science.gov (United States)

    An intracellular plant pathogen ‘Ca. Liberibacter asiaticus,’ a member of the Rhizobiales, is related to Sinorhizobium meliloti, Bradyrhizobium japonicum, Agrobacterium tumefaciens and Bartonella henselae, an intracellular mammalian pathogen. Whole chromosome comparisons identified at least 52 clust...

  12. ORF Alignment: NC_003063 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available PHA-GLUCAN BRANCHING ENZYME (GLYCOGEN BRANCHING ... ENZYME) PROTEIN [Sinorhizobium meliloti] ... ... ... ref|NP_386950.1| PROBABLE 1,4-ALPHA-GLUCAN BRANCHING ... ENZYME (GLYCOGEN BRANCHING ENZYME) PROTEI

  13. ORF Alignment: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available PHA-GLUCAN BRANCHING ENZYME (GLYCOGEN BRANCHING ... ENZYME) PROTEIN [Sinorhizobium meliloti] ... ... ... ref|NP_386950.1| PROBABLE 1,4-ALPHA-GLUCAN BRANCHING ... ENZYME (GLYCOGEN BRANCHING ENZYME) PROTEI

  14. ORF Alignment: NC_003305 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available PHA-GLUCAN BRANCHING ENZYME (GLYCOGEN BRANCHING ... ENZYME) PROTEIN [Sinorhizobium meliloti] ... ... ... ref|NP_386950.1| PROBABLE 1,4-ALPHA-GLUCAN BRANCHING ... ENZYME (GLYCOGEN BRANCHING ENZYME) PROTEI

  15. ORF Alignment: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003047 gi|15965983 >1bu6Y 1 436 4 408 6e-44 ... emb|CAC46809.1| PUTATIVE CARBOHYDRATE... KINASE PROTEIN [Sinorhizobium meliloti] ... ref|NP_386336.1| PUTATIVE CARBOHYDRATE KINASE PROTEIN

  16. ORF Alignment: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003047 gi|15965553 >1rkd0 3 268 9 275 2e-23 ... emb|CAC46379.1| PUTATIVE CARBOHYDRATE... KINASE PROTEIN [Sinorhizobium meliloti] ... ref|NP_385906.1| PUTATIVE CARBOHYDRATE KINASE PROTEIN

  17. ORF Alignment: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available MOYL-PHOSPHATE SYNTHASE LARGE CHAIN (AMMONIA CHAIN ... ARGININE BIOSYNTHESIS) PROTEIN [Sinorhizobium... meliloti] ... ref|NP_385682.1| PROBABLE CARBAMOYL-PHOSPHATE SYNTHASE ... LARGE CHAIN (AMMONIA

  18. ORF Sequence: NC_003047 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003047 gi|15965329 >gi|15965329|ref|NP_385682.1| PROBABLE CARBAMOYL-PHOSPHATE SYNTHASE LARGE CHAIN (AMMO...NIA CHAIN ARGININE BIOSYNTHESIS) PROTEIN [Sinorhizobium meliloti 1021] MPKRQDIKSILI

  19. Comparison of muscle-to-nodule and parenchyma-to-nodule strain ratios in the differentiation of benign and malignant thyroid nodules: Which one should we use?

    Energy Technology Data Exchange (ETDEWEB)

    Aydin, Ramazan, E-mail: raydin1984@hotmail.com [Department of Radiology, Samsun Education and Research Hospital, Samsun (Turkey); Elmali, Muzaffer, E-mail: muzafel@yahoo.com.tr [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Polat, Ahmet Veysel, E-mail: veyselp@hotmail.com [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Danaci, Murat, E-mail: danacim55@yahoo.com [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Akpolat, Ilkser, E-mail: ilkserakpolat@yahoo.com [Department of Pathology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey)

    2014-03-15

    Objective: The aim of this study is to investigate the diagnostic accuracy of muscle-to-nodule strain ratio (MNSR) in the differentiation of benign and malignant thyroid nodules and to see if there was a difference between MNSR and parenchyma-to-nodule strain ratios (PNSR) in diagnosis. Methods: A total of 106 consecutive patients (88 women and 18 men; age range 19–79 years) with thyroid nodules were prospectively examined using ultrasound and sonoelastography before the fine-needle aspiration biopsy. The mean MNSR and PNSR were calculated for each nodule and the elasticity score was determined according to four-point scoring system. Results: According to the four-point scoring system, 44 of the 83 benign nodules had a score of one or two while 22 of the 23 malignant nodules had a score of three or four (p < 0.001). Using ROC analysis, the best cutoff point for MNSR 1.85 and for PNSR 3.14 was calculated. The sensitivity and specificity for the MNSR were 95.6%, 92.8%, respectively; for the PNSR were 95.6%, 93.4%, respectively, when the best cutoff points were used (p < 0.001). The κ value for the PNSR and MNSR methods was 0.87, which indicated an almost perfect agreement (p < 0.001). Conclusions: Sonoelastography has a high diagnostic accuracy in the differentiation of benign and malignant thyroid nodules. There was no significant difference between MNSR and PNSR in the differentiation of benign and malignant thyroid nodules. Therefore, we think that MNSR could safely be used in situations where PNSR could not be used.

  20. Vasculature surrounding a nodule: A novel lung cancer biomarker.

    Science.gov (United States)

    Wang, Xiaohua; Leader, Joseph K; Wang, Renwei; Wilson, David; Herman, James; Yuan, Jian-Min; Pu, Jiantao

    2017-12-01

    To investigate whether the vessels surrounding a nodule depicted on non-contrast, low-dose computed tomography (LDCT) can discriminate benign and malignant screen detected nodules. We collected a dataset consisting of LDCT scans acquired on 100 subjects from the Pittsburgh Lung Screening study (PLuSS). Fifty subjects were diagnosed with lung cancer and 50 subjects had suspicious nodules later proven benign. For the lung cancer cases, the location of the malignant nodule in the LDCT scans was known; while for the benign cases, the largest nodule in the LDCT scan was used in the analysis. A computer algorithm was developed to identify surrounding vessels and quantify the number and volume of vessels that were connected or near the nodule. A nonparametric receiver operating characteristic (ROC) analysis was performed based on a single nodule per subject to assess the discriminability of the surrounding vessels to provide a lung cancer diagnosis. Odds ratio (OR) were computed to determine the probability of a nodule being lung cancer based on the vessel features. The areas under the ROC curves (AUCs) for vessel count and vessel volume were 0.722 (95% CI=0.616-0.811, plung cancer group 9.7 (±9.6) compared to the non-lung cancer group 4.0 (±4.3) CONCLUSION: Our preliminary results showed that malignant nodules are often surrounded by more vessels compared to benign nodules, suggesting that the surrounding vessel characteristics could serve as lung cancer biomarker for indeterminate nodules detected during LDCT lung cancer screening using only the information collected during the initial visit. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. VATS intraoperative tattooing to facilitate solitary pulmonary nodule resection

    Directory of Open Access Journals (Sweden)

    Boutros Cherif

    2008-03-01

    Full Text Available Abstract Introduction Video-assisted thoracic surgery (VATS has become routine and widely accepted for the removal of solitary pulmonary nodules of unknown etiology. Thoracosopic techniques continue to evolve with better instruments, robotic applications, and increased patient acceptance and awareness. Several techniques have been described to localize peripheral pulmonary nodules, including pre-operative CT-guided tattooing with methylene blue, CT scan guided spiral/hook wire placement, and transthoracic ultrasound. As pulmonary surgeons well know, the lung and visceral pleura may appear featureless on top of a pulmonary nodule. Case description This paper presents a rapid, direct and inexpensive approach to peripheral lung lesion resection by marking the lung parenchyma on top of the nodule using direct methylene blue injection. Methods In two patients with peripherally located lung nodules (n = 3 scheduled for VATS, we used direct methylene blue injection for intraoperative localization of the pulmonary nodule. Our technique was the following: After finger palpation of the lung, a spinal 25 gauge needle was inserted through an existing port and 0.1 ml of methylene blue was used to tattoo the pleura perpendicular to the localized nodule. The methylene blue tattoo immediately marks the lung surface over the nodule. The surgeon avoids repeated finger palpation, while lining up stapler, graspers and camera, because of the visible tattoo. Our technique eliminates regrasping and repalpating the lung once again to identify a non marked lesion. Results Three lung nodules were resected in two patients. Once each lesion was palpated it was marked, and the area was resected with security of accurate localization. All lung nodules were resected in totality with normal lung parenchymal margins. Our technique added about one minute to the operative time. The two patients were discharged home on the second postoperative day, with no morbidity. Conclusion

  2. Acoustic radiation force impulse imaging for differentiation of thyroid nodules.

    Directory of Open Access Journals (Sweden)

    Joerg Bojunga

    Full Text Available BACKGROUND: Acoustic Radiation Force Impulse (ARFI-Imaging is an ultrasound-based elastography method enabling quantitative measurement of tissue stiffness. The aim of the present study was to evaluate sensitivity and specificity of ARFI-imaging for differentiation of thyroid nodules and to compare it to the well evaluated qualitative real-time elastography (RTE. METHODS: ARFI-imaging involves the mechanical excitation of tissue using acoustic pulses to generate localized displacements resulting in shear-wave propagation which is tracked using correlation-based methods and recorded in m/s. Inclusion criteria were: nodules ≥5 mm, and cytological/histological assessment. All patients received conventional ultrasound, real-time elastography (RTE and ARFI-imaging. RESULTS: One-hundred-fifty-eight nodules in 138 patients were available for analysis. One-hundred-thirty-seven nodules were benign on cytology/histology, and twenty-one nodules were malignant. The median velocity of ARFI-imaging in the healthy thyroid tissue, as well as in benign and malignant thyroid nodules was 1.76 m/s, 1.90 m/s, and 2.69 m/s, respectively. While no significant difference in median velocity was found between healthy thyroid tissue and benign thyroid nodules, a significant difference was found between malignant thyroid nodules on the one hand and healthy thyroid tissue (p = 0.0019 or benign thyroid nodules (p = 0.0039 on the other hand. No significant difference of diagnostic accuracy for the diagnosis of malignant thyroid nodules was found between RTE and ARFI-imaging (0.74 vs. 0.69, p = 0.54. The combination of RTE with ARFI did not improve diagnostic accuracy. CONCLUSIONS: ARFI can be used as an additional tool in the diagnostic work up of thyroid nodules with high negative predictive value and comparable results to RTE.

  3. Autonomous nodule of the thyroid: correlation of patient age, nodule size, and functional status

    International Nuclear Information System (INIS)

    Blum, M.; Shenkman, L.; Hollander, C.S.

    1975-01-01

    In light of new techniques for measuring circulating thyroid hormones and for studying the thyroid gland, we present our experience with 35 patients with solitary autonomous nodules of the thyroid to define more precisely the clinical course of patients with this disorder. The patients ranged in age from 19 to 80 years and 31 of the 35 were female. Younger patients were generally euthyroid and sought attention because of a thyroid mass; virtually all older patients were hyperthyroid. Eighteen had obvious clinical features of hyperthyroidism and 5 over age 70 had apathetic hyperthyroidism; all 5 of the elderly and 13 of the 18 under age 70 had elevated thyroxine (T 4 ) and triiodothyronine (T 3 ) levels. Isolated elevation of T 3 and elevated basal metabolic rate were observed in 5 previously untreated clinically hyperthyroid young patients. In each of these, thyroid uptake of 131 I was not suppressible with exogenous T 3 and BMR was elevated in those tested. Two elderly patients, who had previously been treated for conventional hyperthyroidism with radioactive iodine, had T 3 toxicosis when hyperthyroidism recurred. There was a strong positive correlation between the age of the patient, the size of the nodule and the thyroid functional state. The mean area of the nodules projected on 131 I rectilinear scan for euthyroid patients was 5.1 cm 2 . The mean area of the nodules in hyperthyroid subjects was significantly higher, 13.4 cm 2 in patients with T 3 toxicosis and 19.3 cm 2 in subjects with conventional hyperthyroidism. Progression from a euthyroid state to hyperthyroidism was observed in four patients. One of these became thyrotoxic within days after an injection of iodinated contrast medium. Spontaneous resolution of nodules occurred in two patients

  4. Guideline on management of solitary pulmonary nodule.

    Science.gov (United States)

    Álvarez Martínez, Carlos J; Bastarrika Alemañ, Gorka; Disdier Vicente, Carlos; Fernández Villar, Alberto; Hernández Hernández, Jesús R; Maldonado Suárez, Antonio; Moreno Mata, Nicolás; Rosell Gratacós, Antoni

    2014-07-01

    The aim of the proposed recommendations is be a tool to facilitate decision-making in patients with a solitary pulmonary nodule (SPN). For an optimal decision, accessibility to the different diagnostics techniques and patient preferences need to be incorporated. The first assessment, which includes a chest computed tomography scan, separates a group of patients with extrapulmonary neoplasm or a high surgical risk who require individualized management. Another two groups of patients are patients with SPN up to 8mm and those who have a subsolid SPN, for which specific recommendations are established. SPN larger than 8mm are classified according to their probability of malignancy into low (less than 5%), where observation is recommended, high (higher than 65%), which are managed with a presumptive diagnosis of localized stage carcinoma, and intermediate, where positron emission tomography-computed tomography has high yield for reclassifying them into high or low probability. In cases of intermediate or high probability of malignancy, transbronchial needle aspiration or biopsy of the nodule may be an option. Radiologic observation with low radiation computed tomography without contrast is recommended in SPN with low probability of malignancy, and resection with videothoracoscopy in undiagnosed cases with intermediate or high probability of malignancy. Copyright © 2013 SEPAR. Published by Elsevier Espana. All rights reserved.

  5. Hydrogen Reactions of Nodulated Leguminous Plants

    Science.gov (United States)

    Schubert, Karel R.; Engelke, Jean A.; Russell, Sterling A.; Evans, Harold J.

    1977-01-01

    The ATP-dependent evolution of H2 catalyzed by nitrogenase and the hydrogenase-catalyzed oxidation of H2 have been implicated as factors influencing the efficiency of energy utilization in the N2 fixation process. The effects of rhizobial strain and plant age on the H2-evolving and H2-utilizing activity of leguminous root nodules are described in this manuscript. Two classes of legume-Rhizobium combinations were observed in studies with soybeans (Glycine max L. Merr.) and cowpeas (Vigna unguiculata L. Walp.). One group evolved H2 in air; the other group did not exhibit net evolution of H2. The latter group metabolized H2 formed within the nodule through the action of a hydrogenase. The capacity to oxidize H2 was strongly linked to the strain of Rhizobium used to inoculate cowpeas and soybeans. Although the magnitude of H2 evolution in air changed during vegetative growth of a given symbiont, the ratio of H2 evolved in air to total nitrogenase activity was not appreciably altered during this period. No consistent difference in nitrogenase activity as measured by the C2H2 reduction assay was observed between symbionts with an active hydrogenase and those that apparently lack the enzyme and evolve H2. The effects of the two reactions of H2 on total N2 fixation and yield must now be established. PMID:16660157

  6. Computerized detection of lung nodules in digital chest radiographs

    International Nuclear Information System (INIS)

    Giger, M.L.; Doi, K.; MacMahon, H.

    1987-01-01

    Detection of cancerous lung nodules in chest radiographs is one of the more important tasks performed by a radiologist. In addition, the ''miss rate'' associated with the radiographic detection of lung nodules is approximately 30%. A computerized scheme that alerts the radiologist to possible locations of lung nodules should allow this number of false-negative diagnoses to be reduced. The authors are developing a computer-aided nodule detection scheme based on a difference image approach. They attempt to eliminate the camouflaging background structure of the normal lung anatomy by creating, from a single-projection chest image, two images: one in which the signal-to-noise ratio (SNR) of the nodule is maximized and another in which that SNR is suppressed while the processed background remains essentially the same. Thus, the difference between these two processed images should consist of the nodule superimposed on a relatively uniform background in which the detection task may be simplified. This difference image approach is fundamentally different from conventional subtraction techniques (e.g., temporal or dual-energy subtraction) in that the two images which are subtracted arise from the same single-projection chest radiograph. Once the difference image is obtained, thresholding is performed along with tests for circularity, size and growth in order to extract the nodules. It should be noted that once an original chest image is input to the computer the nodule detection process is totally automated

  7. The relationship between occupational radiation exposure and thyroid nodules

    Directory of Open Access Journals (Sweden)

    Atoosa Adibi

    2012-01-01

    Full Text Available Background: Considering that thyroid nodules and thyroid cancer occur more frequently in people chronically exposed to radiation, the aim of this study was to evaluate the prevalence of thyroid nodules in a population occupationally exposed to radiation in hospitals of Isfahan, Iran. Materials and Methods: In this case-control study, the prevalence of thyroid nodules in staff members occupationally exposed to radiation was determined by ultrasonography. The results were compared with the results of another study among the adult population of Isfahan which selected by cluster random sampling method. The 2 studied groups were matched according to sex and age. Results: The case and control groups included 124 and 471 persons, respectively. The prevalence of thyroid nodules in the case and control groups was 22.6% and 24.6%, respectively (p > 0.05. Although thyroid nodules were significantly more prevalent in females in the control group, no such difference was observed between females and males of the case group (p > 0.05. The number of thyroid nodules (single or multiple and calcification were not different between the two groups (p > 0.05. In addition, hypoechogenicity of thyroid nodules was not different between the two groups for (p > 0.05. Conclusion: In our study, there was not any correlation between chronic occupational exposure to low dose of radiation and the risk of developing thyroid nodules. Further studies with larger sample sizes, at different doses of radiation, and considering iodine status and thyroid function are thus required.

  8. The relationship between occupational radiation exposure and thyroid nodules

    Science.gov (United States)

    Adibi, Atoosa; Rezazade, Afshin; Hovsepian, Silva; Koohi, Razie; Hosseini, Mohsen

    2012-01-01

    Background: Considering that thyroid nodules and thyroid cancer occur more frequently in people chronically exposed to radiation, the aim of this study was to evaluate the prevalence of thyroid nodules in a population occupationally exposed to radiation in hospitals of Isfahan, Iran. Materials and Methods: In this case-control study, the prevalence of thyroid nodules in staff members occupationally exposed to radiation was determined by ultrasonography. The results were compared with the results of another study among the adult population of Isfahan which selected by cluster random sampling method. The 2 studied groups were matched according to sex and age. Results: The case and control groups included 124 and 471 persons, respectively. The prevalence of thyroid nodules in the case and control groups was 22.6% and 24.6%, respectively (p > 0.05). Although thyroid nodules were significantly more prevalent in females in the control group, no such difference was observed between females and males of the case group (p > 0.05). The number of thyroid nodules (single or multiple) and calcification were not different between the two groups (p > 0.05). In addition, hypoechogenicity of thyroid nodules was not different between the two groups for (p > 0.05). Conclusion: In our study, there was not any correlation between chronic occupational exposure to low dose of radiation and the risk of developing thyroid nodules. Further studies with larger sample sizes, at different doses of radiation, and considering iodine status and thyroid function are thus required. PMID:23626606

  9. A case of cyclist's nodule in a female patient

    African Journals Online (AJOL)

    ere are few reported cases of cyclist's nodule in females. e condition has thus lent itself to synonyms such as third, supernumerary or ... We report the imaging ndings of a perineal nodule in a 29-year-old female patient who is a known cyclist, and discuss ... from vibration and friction between the ischial tuberosities and the.

  10. Germination, growth and nodulation of Trigonella foenum graecum ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... In this work, we analyzed the effects of salinity on seed germination, growth and nodulation of fenugreek plants. The germination of fenugreek seeds was not affected by salt concentrations lower than 140 mM. Two saline tolerant indigenous rhizobia strains were isolated from the root nodules of fenugreek ...

  11. Is genetic selection for skin nodule traits of ostriches feasible ...

    African Journals Online (AJOL)

    Preliminary genetic parameters for nodule traits of ostrich skins were estimated to examine whether genetic improvement of skin quality is feasible. Average nodule size and density per dmยฒ were determined on five localities on each of 439 ostrich skins. An animal model with random animal and skin permanent ...

  12. Uranium in Pacific Deep-Sea Sediments and Manganese Nodules

    DEFF Research Database (Denmark)

    Kunzendorf, Helmar; Pluger, W. L.; Friedrich, G. H.

    1983-01-01

    A total of 1344 manganese nodules and 187 pelagic sediments from 9 areas in the North and the South Pacific were analyzed for U by the delayed-neutron counting technique. A strong positive correlation between U and Fe in nodules and sediments suggests a co-precipitative removal from sea water int...

  13. Variation in nodulation and growth of groundnut ( Arachis hypogaea ...

    African Journals Online (AJOL)

    Improving biological nitrogen fixation through legume nodulating bacteria (LNB) inoculation requires knowledge on the abundance and effectiveness of indigenous population in the ferralsols. Nodulation of groundnut was examined under pots experiment in four location sites of the Humid-forest zone: Bertoua in the East; ...

  14. Germination, growth and nodulation of Trigonella foenum graecum ...

    African Journals Online (AJOL)

    In this work, we analyzed the effects of salinity on seed germination, growth and nodulation of fenugreek plants. The germination of fenugreek seeds was not affected by salt concentrations lower than 140 mM. Two saline tolerant indigenous rhizobia strains were isolated from the root nodules of fenugreek grown in two ...

  15. Occurrence of Nodulation in Leguminous Trees in Kenya | Anyango ...

    African Journals Online (AJOL)

    Exploitation of the potential for nitrogen fixing trees, soil improvement and multipurpose use, requires a good knowledge of their nodulation capabilities and agrosilvicultural manipulation. Nitrogen Fixation in some nodulated species can be maximized by inoculation with effective Rhizobium strains. This study reports the ...

  16. Nodulation potential of four Trifolium repens cultivars under field ...

    African Journals Online (AJOL)

    Four Trifolium repens (white clover) cultivars were evaluated under field conditions to determine the potential of these cultivars to sucessfully develop Rhizobium-associated root nodules. Nodulation of T. repens is often poor, because of suboptimal environmental conditions or absence of host-specific rhizobia. The cultivars ...

  17. Bean nodulation patterns in soils of different texture at Morogoro ...

    African Journals Online (AJOL)

    This study was designed to examine the, relationship between nodulation in a bean-Rhizobium system in three soils of varying texture and % recovery of rhizobia I cells immediately after inoculation into such soils. Effects of inoculation methods (seed pelleting versus soil inoculation) on nodulation and plant growth were ...

  18. Ferric Leghemoglobin in Plant-Attached Leguminous Nodules.

    Science.gov (United States)

    Lee, Kk.; Shearman, L. L.; Erickson, B. K.; Klucas, R. V.

    1995-01-01

    Leghemoglobin (Lb) is essential for nitrogen fixation by intact leguminous nodules. To determine whether ferric Lb (Lb3+) was detectable in nodules under normal or stressed conditions, we monitored the status of Lb in intact nodules attached to sweet clover (Melilotus officinalis) and soybean (Glycine max [L.] Merr.) roots exposed to various conditions. The effects of N2 and O2 streams and elevated nicotinate levels on root-attached nodules were tested to determine whether the spectrophotometric technique was showing the predicted responses of Lb. The soybean and sweet clover nodules' Lb spectra indicated predominantly ferrous Lb and LbO2 in young (34 d) plants. As the nodule aged beyond 45 d, it was possible to induce Lb3+ with a 100% O2 stream (15 min). At 65 d without inducement, the nodule Lb status indicated the presence of some Lb3+ along with ferrous Lb and oxyferrous Lb. Nicotinate and fluoride were used as ligands to identify Lb3+. Computer-calculated difference spectra were used to demonstrate the changes in Lb spectra under different conditions. Some conditions that increased absorbance in the 626 nm region (indicating Lb3+ accumulation) were root-fed ascorbate and dehydroascorbate, plant exposure to darkness, and nodule water immersion. PMID:12228593

  19. Bean Nodulation Patterns in Soils of Different Texture at Morogoro ...

    African Journals Online (AJOL)

    Abstract. This study was designed to examine the, relationship between nodulation in a bean-Rhizobium system in three soils of varying texture and % recovery of rhizobia I cells immediately after in- oculation into such soils. Effects of inoculation methods (seed pelleting versus soil inocula- tion) on nodulation and plant ...

  20. 3D pulmonary nodules detection using fast marching segmentation ...

    African Journals Online (AJOL)

    This paper proposes an automated computer aided diagnosis system for detection of pulmonary nodules based on three dimensional (3D) structures. Lung ... The proposed detection methodology can give the accuracy of 92%. Keywords: lung cancer; pulmonary nodule; fast marching; 3D features; random forest classifier.

  1. Nodulin gene expression during soybean (Glycine max) nodule development.

    NARCIS (Netherlands)

    Gloudemans, T.; Vries, de S.; Bussink, H.J.; Malik, N.S.A.; Franssen, H.; Louwerse, J.; Bisseling, T.

    1987-01-01

    In vitro translation products of total RNA isolated from soybean nodules at successive stages of nodule development were analyzed by two-dimensional gel electrophoresis. In that way the occurrence of over 20 mRNAs specifically transcribed from nodulin genes was detected. The nodulin genes could be

  2. System for automatic detection of lung nodules exhibiting growth

    Science.gov (United States)

    Novak, Carol L.; Shen, Hong; Odry, Benjamin L.; Ko, Jane P.; Naidich, David P.

    2004-05-01

    Lung nodules that exhibit growth over time are considered highly suspicious for malignancy. We present a completely automated system for detection of growing lung nodules, using initial and follow-up multi-slice CT studies. The system begins with automatic detection of lung nodules in the later CT study, generating a preliminary list of candidate nodules. Next an automatic system for registering locations in two studies matches each candidate in the later study to its corresponding position in the earlier study. Then a method for automatic segmentation of lung nodules is applied to each candidate and its matching location, and the computed volumes are compared. The output of the system is a list of nodule candidates that are new or have exhibited volumetric growth since the previous scan. In a preliminary test of 10 patients examined by two radiologists, the automatic system identified 18 candidates as growing nodules. 7 (39%) of these corresponded to validated nodules or other focal abnormalities that exhibited growth. 4 of the 7 true detections had not been identified by either of the radiologists during their initial examinations of the studies. This technique represents a powerful method of surveillance that may reduce the probability of missing subtle or early malignant disease.

  3. Solitary pulmonary nodule: radiologic features and diagnostic approach

    International Nuclear Information System (INIS)

    Rodriguez Cambronero, Luis Enrique

    2012-01-01

    A literature review is conducted on the solitary pulmonary nodule, to determine the diagnostic methods and specific characteristics. The diagnostic methods used have been: chest radiography, computed tomography, positron emission tomography and magnetic resonance imaging. The radiological features are defined: location, size, definition of contours or edges (margins), densitometric and attenuation characteristics, cavitation, air bronchogram, growth, doubling time, satellite nodules, nutrient vessels [es

  4. Vocal nodules in a colombian teachers group with dysphonia

    Directory of Open Access Journals (Sweden)

    Andrés Felipe Alvarado Díaz

    2013-12-01

    Full Text Available Objectives: This study determined the prevalence of vocal nodules associated with dysphonia in teachers aged from 35 to 65 years, taking into consideration both individual and occupational variables. Methodology: Descriptive study that included the information contained in 262 medical records of teachers diagnosed with dysphonia in occupational health consultations at the institutions that provide health services in Bogotá, Colombia from March 2009 to March 2012. The presence of laryngeal nodules was based on the findings of a nasofibrolaryngoscopy procedure. Results: Nodules were found in 67 teachers, which corresponded to a rate of 25.5%, being apparently (highest observed rates associated primarily with the following variables: females, ages from 45 to 54 years, bilateral nodules, and teaching position (preschool and physical education. Of the teachers with nodules, 76.1% had fewer than five doctor's appointments, and 75% had more than 90 days of sick leave. Conclusion: A high percentage of teachers have vocal nodules associated with dysphonia. This may be apparently related to different variables such as sex, type of nodule, area and teaching position. Was observed only a statistically significant association among presence of nodules and age (p=0.018. In addition this disorder generates a large number of incapacities and employee absenteeism.

  5. Management of subsolid pulmonary nodules in CT lung cancer screening

    NARCIS (Netherlands)

    Heuvelmans, Marjolein A.; Oudkerk, Matthijs

    The distinct appearance and behavior of subsolid pulmonary nodules (SSNs) has resulted in separate recommendations for the management of solitary SSNs, both for incidentally detected as well as for screen detected nodules. However, these guidelines have been based primarily on expert opinion.

  6. Internal microfeatures of manganese nodules from the Central Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Pattan, J.N.

    whereas nodules from the abyssal plains show prominent, well-developed columnar structures. Features such as botryoids and fractures filled with Fe and Mn oxides are more common in the nodules of abyssal plains whereas the clay content and clastic grains...

  7. Danish Rhizobium leguminosarum strains nodulating ‘Afghanistan’ pea (Pisum sativum)

    DEFF Research Database (Denmark)

    Jensen, Erik Steen; Sørensen, Lasse Holst; Engvild, Kjeld Christensen

    1986-01-01

    A wild pea (Pisum sativum L.) native to Afghanistan normally known to be resisant to nodulation with European strains of Rhizobium leguminosarum was nodulated early and effectively in field soil in Denmark. Isolates from nodules formed effective nodules abundantly on 'Afghanistan' on reinfection ...... pattern with Rhizobium leguminosarum strains isolated from a modern pea variety cultivated in the same field.......A wild pea (Pisum sativum L.) native to Afghanistan normally known to be resisant to nodulation with European strains of Rhizobium leguminosarum was nodulated early and effectively in field soil in Denmark. Isolates from nodules formed effective nodules abundantly on 'Afghanistan' on reinfection...

  8. Quantitative image measurements for outcome analysis of lung nodule treatment

    Science.gov (United States)

    Zhu, Xiaoming; Lee, Ki-Nam; Wong, Stephen T. C.; Huang, H. K.

    1996-04-01

    In this study, we designed and implemented a temporal image database for outcome analysis of lung nodules based on spiral CT images. The software package is composed of three parts. They are, respectively, a database management system which stores patient image data and nodule information; a user-friendly graphical user interface which allows a user to interface with the image database; and image processing tools that are designed to segment out lung nodules in the CT image with a simple mouse click anywhere inside a nodule. The image database uses the relational Sybase database system. Patient images and nodule information are stored in separate tables. Software interface has been designed to allow a user to retrieve any patient study from the picture archiving and communication system into the image database.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Nitrogen fixation and carbon metabolism in legume nodules.

    Science.gov (United States)

    Garg, Neera; Singla, Ranju; Geetanjali

    2004-02-01

    A large amount of energy is utilized by legume nodules for the fixation of nitrogen and assimilation of fixed nitrogen (ammonia) into organic compounds. The source of energy is provided in the form of photosynthates by the host plant. Phosphoenol pyruvate carboxylase (PEPC) enzyme, which is responsible for carbon dioxide fixation in C4 and crassulacean acid metabolism plants, has also been found to play an important role in carbon metabolism in legume root nodule. PEPC-mediated CO2 fixation in nodules results in the synthesis of C4 dicarboxylic acids, viz. aspartate, malate, fumarate etc. which can be transported into bacteroids with the intervention of dicarboxylate transporter (DCT) protein. PEPC has been purified from the root nodules of few legume species. Information on the relationship between nitrogen fixation and carbon metabolism through PEPC in leguminous plants is scanty and incoherent. This review summarizes the various aspects of carbon and nitrogen metabolism in legume root nodules.

  11. Direct detection of radicals in intact soybean nodules

    DEFF Research Database (Denmark)

    Mathieu, C; Moreau, S; Frendo, P

    1998-01-01

    Electron paramagnetic resonance spectroscopy has been employed to examine the nature of the metal ions and radicals present in intact root nodules of soybean plants grown in the absence of nitrate. The spectra obtained from nodules of different ages using this non-invasive technique show dramatic...... differences, suggesting that there are both qualitative and quantitative changes in the metal ion and radical species present. A major component of the spectra obtained from young nodules is assigned to a complex (Lb-NO) of nitric oxide (NO.) with the heme protein leghemoglobin (Lb). This Lb-NO species, which...... has not been previously detected in intact root nodules of plants grown in the absence of nitrate, is thought to be formed by reaction of nitric oxide with iron(II) leghemoglobin. The nitric oxide may be generated from arginine via a nitric oxide synthase-like activity present in the nodules...

  12. Volumetric measurements of pulmonary nodules: variability in automated analysis tools

    Science.gov (United States)

    Juluru, Krishna; Kim, Woojin; Boonn, William; King, Tara; Siddiqui, Khan; Siegel, Eliot

    2007-03-01

    Over the past decade, several computerized tools have been developed for detection of lung nodules and for providing volumetric analysis. Incidentally detected lung nodules have traditionally been followed over time by measurements of their axial dimensions on CT scans to ensure stability or document progression. A recently published article by the Fleischner Society offers guidelines on the management of incidentally detected nodules based on size criteria. For this reason, differences in measurements obtained by automated tools from various vendors may have significant implications on management, yet the degree of variability in these measurements is not well understood. The goal of this study is to quantify the differences in nodule maximum diameter and volume among different automated analysis software. Using a dataset of lung scans obtained with both "ultra-low" and conventional doses, we identified a subset of nodules in each of five size-based categories. Using automated analysis tools provided by three different vendors, we obtained size and volumetric measurements on these nodules, and compared these data using descriptive as well as ANOVA and t-test analysis. Results showed significant differences in nodule maximum diameter measurements among the various automated lung nodule analysis tools but no significant differences in nodule volume measurements. These data suggest that when using automated commercial software, volume measurements may be a more reliable marker of tumor progression than maximum diameter. The data also suggest that volumetric nodule measurements may be relatively reproducible among various commercial workstations, in contrast to the variability documented when performing human mark-ups, as is seen in the LIDC (lung imaging database consortium) study.

  13. Impact of overexpression of cytosolic isoform of O-acetylserine sulfhydrylase on soybean nodulation and nodule metabolome

    Science.gov (United States)

    Nitrogen-fixing nodules, which are also major sites of sulfur assimilation, contribute significantly to the sulfur needs of the whole soybean plants. Nodules are the predominant sites for cysteine accumulation and the activity of O-acetylserine sulfhydrylase (OASS; also known as O-acetylserine(thio...

  14. The Effects of Clinorotation on the Host Plant, Medicago truncatula, and Its Microbial Symbionts

    Energy Technology Data Exchange (ETDEWEB)

    Dauzart, Ariel J. C.; Vandenbrink, Joshua P.; Kiss, John Z., E-mail: jzkiss@olemiss.edu [Department of Biology, Graduate School, University of Mississippi, University, MS (United States)

    2016-02-26

    Understanding the outcome of the plant-microbe symbiosis in reduced or altered is vital to developing life support systems for long-distance space travel and colonization of other planets. Thus, the aim of this research was to understand mutualistic relationships between plants and endophytic microbes under the influence of altered gravity. This project utilized the model tripartite relationship among Medicago truncatula—Sinorhizobium meliloti—Rhizophagus irregularis. Plants were inoculated with rhizobial bacteria (S. meliloti), arbuscular mycorrhizal fungi (R. irregularis), or both microbes, and placed on a rotating clinostat. Vertical and horizontal static controls were also performed. Clinorotation significantly reduced M. truncatula dry mass and fresh mass compared to the static controls. The addition of rhizobia treatments under clinorotation also altered total root length and root-to-shoot fresh mass ratio. Nodule size decreased under rhizobia + clinorotation treatment, and nodule density was significantly decreased compared to the vertical treatment. However, inoculation with arbuscular mycorrhizal fungi was shown to increase biomass accumulation and nodule size. Thus, clinorotation significantly affected M. truncatula and its symbiotic relationships with S. meliloti and R. irregularis. In the long term, the results observed in this clinostat study on the changes of plant-microbe mutualism need to be investigated in spaceflight experiments. Thus, careful consideration of the symbiotic microbes of plants should be included in the design of bioregenerative life support systems needed for space travel.

  15. Predictive factors for malignancy in incidental pulmonary nodules detected in breast cancer patients at baseline CT

    Energy Technology Data Exchange (ETDEWEB)

    Hammer, Mark M.; Mortani Barbosa, Eduardo J. [University of Pennsylvania, Division of Cardiothoracic Imaging, Department of Radiology, Perelman School of Medicine, Philadelphia, PA (United States)

    2017-07-15

    Pulmonary nodules are commonly encountered at staging CTs in patients with extrathoracic malignancies, but their significance on a per-patient basis remains uncertain. We undertook a retrospective analysis of pulmonary nodules identified in patients with a diagnosis of breast cancer from 2010 - 2015, evaluating nodules present at a baseline CT (i.e. prevalent nodules). We reviewed 211 patients with 248 individual nodules. The rate of malignancy in prevalent nodules is low, approximately 13 %. Variables associated with metastasis include pleural studding, hilar lymphadenopathy and the presence of extrapulmonary metastasis, as well as number of nodules, nodule size and nodule shape. Using a combination of these factors, we have developed an evidence-based multivariate decision tree to predict which nodules are malignant in these patients, which is 91 % accurate and 100 % sensitive for metastasis. We propose a simplified clinical prediction algorithm to guide radiologists and oncologists in managing patients with breast cancer and incidental pulmonary nodules. (orig.)

  16. Graphite nodule count and size distribution in thin-walled ductile cast iron

    DEFF Research Database (Denmark)

    Pedersen, Karl Martin; Tiedje, Niels Skat

    2008-01-01

    Graphite nodule count and size distribution have been analysed in thin walled ductile cast iron. The 2D nodule counts have been converted into 3D nodule count by using Finite Difference Method (FDM). Particles having a diameter smaller than 5 µm should be neglected in the nodule count...... as these are inclusions and micro porosities that do not influence the solidification morphology. If there are many small graphite nodules as in thin walled castings only 3D nodule count calculated by FDM will give reliable results. 2D nodule count and 3D nodule count calculated by simple equations will give too low...... results. The 3D size distribution showed presence of primary graphite nodules in hypereutectic castings. In thin plates the nodule count is similar in eutectic and hypereutectic plates. In thicker plates the hypereutectic casting has the highest nodule count....

  17. Development of a clinical decision model for thyroid nodules

    Directory of Open Access Journals (Sweden)

    Eberhardt John

    2009-08-01

    Full Text Available Abstract Background Thyroid nodules represent a common problem brought to medical attention. Four to seven percent of the United States adult population (10–18 million people has a palpable thyroid nodule, however the majority (>95% of thyroid nodules are benign. While, fine needle aspiration remains the most cost effective and accurate diagnostic tool for thyroid nodules in current practice, over 20% of patients undergoing FNA of a thyroid nodule have indeterminate cytology (follicular neoplasm with associated malignancy risk prevalence of 20–30%. These patients require thyroid lobectomy/isthmusectomy purely for the purpose of attaining a definitive diagnosis. Given that the majority (70–80% of these patients have benign surgical pathology, thyroidectomy in these patients is conducted principally with diagnostic intent. Clinical models predictive of malignancy risk are needed to support treatment decisions in patients with thyroid nodules in order to reduce morbidity associated with unnecessary diagnostic surgery. Methods Data were analyzed from a completed prospective cohort trial conducted over a 4-year period involving 216 patients with thyroid nodules undergoing ultrasound (US, electrical impedance scanning (EIS and fine needle aspiration cytology (FNA prior to thyroidectomy. A Bayesian model was designed to predict malignancy in thyroid nodules based on multivariate dependence relationships between independent covariates. Ten-fold cross-validation was performed to estimate classifier error wherein the data set was randomized into ten separate and unique train and test sets consisting of a training set (90% of records and a test set (10% of records. A receiver-operating-characteristics (ROC curve of these predictions and area under the curve (AUC were calculated to determine model robustness for predicting malignancy in thyroid nodules. Results Thyroid nodule size, FNA cytology, US and EIS characteristics were highly predictive of

  18. Pulmonary nodules and metastases in colorectal cancer

    DEFF Research Database (Denmark)

    Nordholm-Carstensen, Andreas

    2016-01-01

    Patients with newly diagnosed colorectal cancer (CRC) are subjected to a preoperative thoraco-abdominal CT scan to determine the cancer stage. This staging is of relevance with regard to treatment and prognosis. About 20% of the patients have distant metastatic spread at the time of diagnosis, i...... is minimal. Furthermore, the current staging practice is complicated by a high number of incidental findings on the thoracic CT, so-called indeterminate pulmonary nodules (IPN). IPN can potentially represent SPCM. The purpose of this thesis was to estimate the prevalence, characteristics and clinical...... 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...

  19. Indeterminate Pulmonary Nodules in Colorectal-Cancer

    DEFF Research Database (Denmark)

    Nordholm-Carstensen, Andreas; Jorgensen, Lars N; Wille-Jørgensen, Peer A

    2015-01-01

    BACKGROUND: The clinical significance of indeterminate pulmonary nodules (IPN) at staging computed tomography (CT) for colorectal cancer (CRC), and the optimal diagnostic approach, are debated. This study aimed to analyse variability in radiologists' detection of IPN at staging CT for CRC. METHODS......: All patients with CRC referred to our center between 2006 and 2011 were included. Primary staging CT scans were re-evaluated by an experienced thoracic radiologist whose findings were entered into a dedicated database and merged with data from the Danish Colorectal Cancer Group database, the National...... investigated radiological characteristics or clinicopathological factors were significantly associated with malignancy of IPN. CONCLUSION: The characterization of pulmonary findings on staging CT for CRC varied greatly between the radiologists, and double-reading of scans with IPN is recommended prior...

  20. Thyroid nodule and the value of tumormarkers

    International Nuclear Information System (INIS)

    Goerges, R.; Bockisch, A.

    2008-01-01

    According to common scientific opinion thyroglobulin (hTg) is not recommended as a tumor marker for clarifying the dignity of thyroid nodules, due to a strong overlap between values of differentiated thyroid carcinoma (DTC) and benign thyroid nodules. Moreover, other benign thyroid diseases with cellular lesion, i.e. nodules and overt inflammation, lead to significantly increased thyroglobulin values (values in a four-digit range and even more in very rare cases). The determination of hTg before thyroid ablation can be a useful ''screening marker'' for patients with CUP-syndrome and suspicious thyroid lesions to identify subjects suffering under DTC. Furthermore, in the case of DTC preoperatively measured hTg will help to validate and evaluate hTg values in the follow-up of these patients. hTg determination can be disturbed by methodological artefacts, in particular by interfering anti-hTg auto-antibodies. For the authentication of hTg values anti-hTg auto-antibody measurement and/or recovery testing is therefore essential although both methods have advantages and disadvantages in that respect. Calcitonin (hCt) is a relatively reliable and specific marker for medullary thyroid carcinoma (MTC) or neoplastic C-cell hyperplasia provided that optimal techniques and appropriate interpretation of test results are applied. The use of two-site assays with a high specificity for the monomer molecule is advised, but false-positive values can still occur, i.e. in renal insufficiency, during therapy with proton pump inhibitors, in goiters with ''physiological'' C-cell hyperplasia and in autoimmune thyroiditis. The Thyroid Section of the German Society of Endocrinology recommends hCt-screening for patients with nodular goiter although some questions regarding epidemiology, health economy and methodology are not resolved yet. Basal hCT values exceeding 100 pg/ml are highly predictive for MTC after exclusion of the reasons mentioned above which can cause artificially increased

  1. Subcutaneous nodule: A case of Dirofilaria

    Science.gov (United States)

    D’Souza, Reshmina; Jakribettu, Ramakrishna Pai; Sudharsana, Sunil H; Aithala, Sathyamoorthy P

    2013-01-01

    Human subcutaneous dirofilariasis is a rare helminthic infection. It is caused by filarial worms of the Genus Dirofilaria, which is the natural parasites of dogs, cats, foxes, and wild mammals. Zoonotic filariasis caused by Dirofilaria species is rarely seen in the region of Dakshina Kannada. Most of them are seen in patients who are along the border of the district which shares its boundary with the state of Kerala, where dirofilariasis is constantly reported to occur. Here, we report a case of subcutaneous dirofilariasis, presenting as a subcutaneous nodule on the left cheek of a 28-year-old male from Cochin (Ernakulam), Kerala, South India. Two live worms were recovered from the subcutaneous nodular swelling. PMID:23776842

  2. Pulmonary nodules and metastases in colorectal cancer.

    Science.gov (United States)

    Nordholm-Carstensen, Andreas

    2016-01-01

    Patients with newly diagnosed colorectal cancer (CRC) are subjected to a preoperative thoraco-abdominal CT scan to determine the cancer stage. This staging is of relevance with regard to treatment and prognosis. About 20% of the patients have distant metastatic spread at the time of diagnosis, i.e. synchronous metastases. Most common are hepatic metastases followed by pulmonary involvement. The optimal staging modality for detecting synchronous pulmonary metastases is debated. It has been argued, that synchronous pulmonary metastases (SPCM) are rare in CRC and that the consequence of detecting SPCM is minimal. Furthermore, the current staging practice is complicated by a high number of incidental findings on the thoracic CT, so-called indeterminate pulmonary nodules (IPN). IPN can potentially represent SPCM. The purpose of this thesis was to estimate the prevalence, characteristics and clinical significance of IPN and SPCM detected at the primary staging in CRC. Study I was a systematic review of published studies on IPN in CRC focusing on the prevalence and radiological characteristics of IPN proving to be malignant. This knowledge would be of value in management strategies for IPN. On average 9% of all patients staged with a thoracic CT had IPN, however, the prevalence varied significantly between patients series. This was mainly attributed to varying/lacking definitions on IPN and variable radiological expertise in the assessment of the scans. Data were too inconsistently reported in the case series for a robust statement to be made on potential radiological characteristics suggestive of malignancy in IPN. Lymph node metastasis was the most common clinicopathological finding associated with malignancy of IPN. In conclusion, one patient of every 100 scanned patients had an IPN proving to a SPCM at follow-up, but we found no evidence that IPN should result in intensified diagnostic work-up besides routine follow-up for CRC. Study II was an analysis of the

  3. Pulmonary nodules: a quantitative method of diagnosis by evaluating nodule perimeter difference to approximate oval using three-dimensional CT images.

    Science.gov (United States)

    Kamiya, Hisashi; Murayama, Sadayuki; Kakinohana, Yasumasa; Miyara, Tetsuhiro

    2011-01-01

    The purpose of this study was to investigate whether maximum nodule perimeter to the approximate oval could discriminate benign nodules from malignancy. Measurement of maximum nodule perimeter difference to the approximate oval was performed using volume-rendering images of three directions of each pulmonary nodule. The margin was then traced manually and our custom software delineated the approximate oval automatically. The maximum nodule perimeter difference was 26.5±23.3 mm for malignant and 16.6±16.9 mm for benign nodules, showing an almost statistically significant difference (P=.07). This study suggests that the maximum nodule perimeter difference to the approximate oval of the malignant nodules has a tendency to be longer than benign nodules. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Pulmonary nodule characterization, including computer analysis and quantitative features.

    Science.gov (United States)

    Bartholmai, Brian J; Koo, Chi Wan; Johnson, Geoffrey B; White, Darin B; Raghunath, Sushravya M; Rajagopalan, Srinivasan; Moynagh, Michael R; Lindell, Rebecca M; Hartman, Thomas E

    2015-03-01

    Pulmonary nodules are commonly detected in computed tomography (CT) chest screening of a high-risk population. The specific visual or quantitative features on CT or other modalities can be used to characterize the likelihood that a nodule is benign or malignant. Visual features on CT such as size, attenuation, location, morphology, edge characteristics, and other distinctive "signs" can be highly suggestive of a specific diagnosis and, in general, be used to determine the probability that a specific nodule is benign or malignant. Change in size, attenuation, and morphology on serial follow-up CT, or features on other modalities such as nuclear medicine studies or MRI, can also contribute to the characterization of lung nodules. Imaging analytics can objectively and reproducibly quantify nodule features on CT, nuclear medicine, and magnetic resonance imaging. Some quantitative techniques show great promise in helping to differentiate benign from malignant lesions or to stratify the risk of aggressive versus indolent neoplasm. In this article, we (1) summarize the visual characteristics, descriptors, and signs that may be helpful in management of nodules identified on screening CT, (2) discuss current quantitative and multimodality techniques that aid in the differentiation of nodules, and (3) highlight the power, pitfalls, and limitations of these various techniques.

  5. Frequency of Thyroid Nodules among Patients with Colonic Polyps

    Directory of Open Access Journals (Sweden)

    Cevdet Duran

    2012-01-01

    Full Text Available Aim. Colonic polyps and thyroid nodules are common diseases and their frequency increases with age. In the literature, there is no study investigating the coexistence of colonic polyps and thyroid nodules. Therefore, this study was designed to investigate thyroid nodule prevalence in patients with colonic polyps. Material and Methods. Sixty-six patients with colonic polyps and 146 patients without colonic polyps enrolled into the study. Age and sex matched control group was composed from patients without colonic polyps. Colonoscopic examinations, thyroid ultrasonographies were performed in all patients, and TSH were measured. Results. Male/female ratio in polyp and control groups were 40/26 versus 68/78, respectively (P=0.058. Mean ages were similar in both groups (53.3±11.4 versus, 51.8±11.4, P=0.373. Thyroid nodule was detected in 44 (66.7% patients with polyps and in 61 (41.8% controls (P=0.001. Patients with adenomatous polyps had 5 or more thyroid nodules compared to patients with hyperplastic polyps (P=0.03. Thyroid nodules were more prevalent among patients aged 50 or older compared to 50 years or less (P=0.023. Conclusion. Thyroid nodules were detected more common in patients with colonic polyps. Further studies are needed to clarify this coexistence.

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

    Directory of Open Access Journals (Sweden)

    Chandra Kant

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  8. Danish Rhizobium leguminosarum strains nodulating ‘Afghanistan’ pea (Pisum sativum)

    DEFF Research Database (Denmark)

    Jensen, Erik Steen; Sørensen, Lasse Holst; Engvild, Kjeld Christensen

    1986-01-01

    A wild pea (Pisum sativum L.) native to Afghanistan normally known to be resisant to nodulation with European strains of Rhizobium leguminosarum was nodulated early and effectively in field soil in Denmark. Isolates from nodules formed effective nodules abundantly on 'Afghanistan' on reinfection...... pattern with Rhizobium leguminosarum strains isolated from a modern pea variety cultivated in the same field....

  9. Genetic variation in nodule size at different sites on the skins of ...

    African Journals Online (AJOL)

    Apart from the limitations evident from these results, the objective measurement of nodules on ostrich skins is tedious when done manually, with little prospect for automation. The number of nodules per dm² (nodule density) was considered within skin sites as an indirect criterion for the improvement of nodule size. However ...

  10. Persistent pulmonary subsolid nodules: model-based iterative reconstruction for nodule classification and measurement variability on low-dose CT.

    Science.gov (United States)

    Kim, Hyungjin; Park, Chang Min; Kim, Seong Ho; Lee, Sang Min; Park, Sang Joon; Lee, Kyung Hee; Goo, Jin Mo

    2014-11-01

    To compare the pulmonary subsolid nodule (SSN) classification agreement and measurement variability between filtered back projection (FBP) and model-based iterative reconstruction (MBIR). Low-dose CTs were reconstructed using FBP and MBIR for 47 patients with 47 SSNs. Two readers independently classified SSNs into pure or part-solid ground-glass nodules, and measured the size of the whole nodule and solid portion twice on both reconstruction algorithms. Nodule classification agreement was analyzed using Cohen's kappa and compared between reconstruction algorithms using McNemar's test. Measurement variability was investigated using Bland-Altman analysis and compared with the paired t-test. Cohen's kappa for inter-reader SSN classification agreement was 0.541-0.662 on FBP and 0.778-0.866 on MBIR. Between the two readers, nodule classification was consistent in 79.8 % (75/94) with FBP and 91.5 % (86/94) with MBIR (p = 0.027). Inter-reader measurement variability range was -5.0-2.1 mm on FBP and -3.3-1.8 mm on MBIR for whole nodule size, and was -6.5-0.9 mm on FBP and -5.5-1.5 mm on MBIR for solid portion size. Inter-reader measurement differences were significantly smaller on MBIR (p = 0.027, whole nodule; p = 0.011, solid portion). MBIR significantly improved SSN classification agreement and reduced measurement variability of both whole nodules and solid portions between readers. • Low-dose CT using MBIR algorithm improves reproducibility in the classification of SSNs. • MBIR would enable more confident clinical planning according to the SSN type. • Reduced measurement variability on MBIR allows earlier detection of potentially malignant nodules.

  11. Molecular characterization of the pSinB plasmid of the arsenite oxidizing, metallotolerant Sinorhizobium sp. M14 - insight into the heavy metal resistome of sinorhizobial extrachromosomal replicons.

    Science.gov (United States)

    Romaniuk, Krzysztof; Dziewit, Lukasz; Decewicz, Przemyslaw; Mielnicki, Sebastian; Radlinska, Monika; Drewniak, Lukasz

    2017-01-01

    Sinorhizobium sp. M14 is an As(III)-oxidizing, psychrotolerant strain, capable of growth in the presence of extremely high concentrations of arsenic and many other heavy metals. Metallotolerant abilities of the M14 strain depend upon the presence of two extrachromosomal replicons: pSinA (∼ 109 kb) and pSinB (∼ 300 kb). The latter was subjected to complex analysis. The performed analysis demonstrated that the plasmid pSinB is a narrow-host-range repABC-type replicon, which is fully stabilized by the phd-vapC-like toxin-antitoxin stabilizing system. In silico analysis showed that among the phenotypic gene clusters of the plasmid pSinB, eight modules are potentially involved in heavy metals resistance (HMR). These modules carry genes encoding efflux pumps, permeases, transporters and copper oxidases, which provide resistance to arsenic, cadmium, cobalt, copper, iron, mercury, nickel, silver and zinc. The functional analysis revealed that the HMR modules are active and have an effect on the minimal inhibitory concentration (MIC) values observed for the heterological host cells. The phenotype was manifested by an increase or decrease of the MICs of heavy metals and it was strain specific. The analysis of distribution of the heavy metal resistance genes, i.e. resistome, in Sinorhizobium spp. plasmids, revealed that the HMR modules are common in these replicons. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. India's manganese nodule mine site in the Central Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Banakar, V.K.

    This commentary highlights the activities of massive exploration programme for manganese nodule deposits in the Central Indian Basin located 5 km below the ocean surface and India's claim for mine site development and registration with UNCLOS...

  13. Direct detection of radicals in intact soybean nodules

    DEFF Research Database (Denmark)

    Mathieu, C; Moreau, S; Frendo, P

    1998-01-01

    Electron paramagnetic resonance spectroscopy has been employed to examine the nature of the metal ions and radicals present in intact root nodules of soybean plants grown in the absence of nitrate. The spectra obtained from nodules of different ages using this non-invasive technique show dramatic...... differences, suggesting that there are both qualitative and quantitative changes in the metal ion and radical species present. A major component of the spectra obtained from young nodules is assigned to a complex (Lb-NO) of nitric oxide (NO.) with the heme protein leghemoglobin (Lb). This Lb-NO species, which......, results in changes in the EPR spectra, with the loss of the signals from the Lb-NO complex and appearance of absorptions similar to those from untreated senescent nodules. These results suggest that there are characteristic changes in both the metal ion complexes and radicals present in intact root...

  14. Ferromanganese nodules from the Central Indian Ocean Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Jauhari, P.; Pattan, J.N.

    In order to delineate a mine site for ferromanganese nodules, extensive surveys were conducted in Central Indian Ocean Basin. Mapping of the basin by multibeam swath bathymetry (Hydrosweep) has revealed many new bottom relief features...

  15. Buried nodules and associated sediments from the central Indian Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Banerjee, R; Iyer, S.D.; Dutta, P.

    Buried nodules from siliceous sediments in the central Indian Basin are morphologically variable and mineralogically consist of d-MnO2 incipient todorokite. Compositionally they are weakly diagenetic. The sediment coarse fractions ( 63 mu m...

  16. The Indian Ocean nodule field: Geology and resource potential

    Digital Repository Service at National Institute of Oceanography (India)

    Mukhopadhyay, R.; Ghosh, A.K.; Iyer, S.D.

    This book briefly accounts for the physiography, geology, biology, physics and chemistry of the nodule field, and discusses in detail the aspects of structure, tectonic and volcanism in the field. The role of the ocean floor sediment that hosts...

  17. Manganese nodules in the Exclusive Economic Zone of Mauritius

    Digital Repository Service at National Institute of Oceanography (India)

    Nath, B.N.; ShyamPrasad, M.

    The distribution of manganese nodules in the Exclusive Economic Zone of the island nation Mauritius was delineated during cruise SK-35 of ORV Sagar Kanya in 1987. The areas surveyed included Saya de Malha and Nazareth Banks, the Cargados Carajos...

  18. Manganese nodules as a possible source of precious metals

    Digital Repository Service at National Institute of Oceanography (India)

    Banerjee, R.

    100 times more Pt. Thus the manganese nodules resources at Central Indian Basin, could be a potential source for precious metals including Pt, Palladium (Pd) and Silver (Ag). In this article the possible precious metal resources present in the Central...

  19. Radiographic test phantom for computed tomographic lung nodule analysis

    International Nuclear Information System (INIS)

    Zerhouni, E.A.

    1987-01-01

    This patent describes a method for evaluating a computed tomograph scan of a nodule in a lung of a human or non-human animal. The method comprises generating a computer tomograph of a transverse section of the animal containing lung and nodule tissue, and generating a second computer tomograph of a test phantom comprising a device which simulates the transverse section of the animal. The tissue simulating portions of the device are constructed of materials having radiographic densities substantially identical to those of the corresponding tissue in the simulated transverse section of the animal and have voids therein which simulate, in size and shape, the lung cavities in the transverse section and which contain a test reference nodule constructed of a material of predetermined radiographic density which simulates in size, shape and position within a lung cavity void of the test phantom the nodule in the transverse section of the animal and comparing the respective tomographs

  20. Scripps Institution of Oceanography Ferromanganese Nodule Analysis File - IDOE Portion

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Scripps Institution of Oceanography (SIO) compiled data on the geochemistry of marine ferromanganese nodules, funded by the U.S. National Science Foundation...

  1. Asparagine Biosynthesis in Alfalfa (Medicago sativa L.) Root Nodules.

    Science.gov (United States)

    Snapp, S S; Vance, C P

    1986-10-01

    Rapid direct conversion of exogenously supplied [(14)C]aspartate to [(14)C] asparagine and to tricarboxylic cycle acids was observed in alfalfa (Medicago sativa L.) nodules. Aspartate aminotransferase activity readily converted carbon from exogenously applied [(14)C]aspartate into the tricarboxylic acid cycle with subsequent conversion to the organic acids malate, succinate, and fumarate. Aminooxyacetate, an inhibitor of aminotransferase activity, reduced the flow of carbon from [(14)C]aspartate into tricarboxylic cycle acids and decreased (14)CO(2) evolution by 99%. Concurrently, maximum conversion of aspartate to asparagine was observed in aminooxyacetate treated nodules (30 nanomoles asparagine per gram fresh weight per hour. Metabolism of [(14)C]aspartate and distribution of nodulefixed (14)CO(2) suggest that two pools of aspartate occur in alfalfa nodules: (a) one involved in asparagine biosynthesis, and (b) another supplying a malate/aspartate shuttle. Conversion of [(14)C]aspartate to [(14)C]asparagine was not inhibited by methionine sulfoximine, a glutamine synthetase inhibitor, or azaserine, a glutmate synthetase, inhibitor. The data did not indicate that asparagine biosynthesis in alfalfa nodules has an absolute requirement for glutamine. Radioactivity in the xylem sap, derived from nodule (14)CO(2) fixation, was markedly decreased by treating nodulated roots with aminooxyacetate, methionine sulfoximine, and azaserine. Inhibitors decreased the [(14)C]aspartate and [(14)]asparagine content of xylem sap by greater than 80% and reduced the total amino nitrogen content of xylem sap (including nonradiolabeled amino acids) by 50 to 80%. Asparagine biosynthesis in alfalfa nodules and transport in xylem sap are dependent upon continued aminotransferase activity and an uninterrupted assimilation of ammonia via the glutamine synthetase/glutamate synthase pathway. Continued assimilation of ammonia apparently appears crucial to continued root nodule CO(2) fixation in

  2. Pulmonary Nodules with Cutaneous Manifestations: A Case Report and Discussion

    Directory of Open Access Journals (Sweden)

    Ardiles T

    2012-04-01

    Full Text Available The differential diagnosis of multiple pulmonary nodules is large and includes congenital and inherited disorders, malignancy, infectious etiologies, noninfectious granulomatous and inflammatory conditions,among many others. Diagnostic evaluation is aided by attention to extrapulmonary symptoms and features. We herein describe an unusual case of multiple pulmonary nodules attributed to cysticercosis and present a discussion of pathophysiologic changes related to medications and highlight the diagnostic value of extrapulmonary cutaneous features.

  3. Pulmonary necrobiotic nodules: a rare extraintestinal manifestation of Crohn's disease

    Directory of Open Access Journals (Sweden)

    G. Warwick

    2009-03-01

    Full Text Available The present article reports the case of a 22-yr-old female with new onset Crohn's colitis, anterior uveitis and multiple pulmonary nodules which, on histological examination, were necrobiotic nodules. This is a rare but recognised pulmonary extraintestinal manifestation of Crohn's disease and only the fourth reported case. The present case report is followed by a brief review of the relevant literature.

  4. Relationship between size and geochemistry of polymetallic nodules from the Central Indian Ocean Basin: Significance in selection of high grade nodules

    Digital Repository Service at National Institute of Oceanography (India)

    Valsangkar, A.B.; Ambre, N.V.

    Morphological, mineralogical and geochemical studies on nodules of different sizes collected from the Central Indian Ocean Basin (CIOB) show two suits of nodule formation by oxic diagenetic and hydrogenous process resulting into distinct properties...

  5. Auto Diagnostics of Lung Nodules Using Minimal Characteristics Extraction Technique

    Directory of Open Access Journals (Sweden)

    Diego M. Peña

    2016-03-01

    Full Text Available Computer-aided detection (CAD systems provide useful tools and an advantageous process to physicians aiming to detect lung nodules. This paper develops a method composed of four processes for lung nodule detection. The first step employs image acquisition and pre-processing techniques to isolate the lungs from the rest of the body. The second stage involves the segmentation process using a 2D algorithm to affect every layer of a scan eliminating non-informative structures inside the lungs, and a 3D blob algorithm associated with a connectivity algorithm to select possible nodule shape candidates. The combinations of these algorithms efficiently eliminate the high rates of false positives. The third process extracts eight minimal representative characteristics of the possible candidates. The final step utilizes a support vector machine for classifying the possible candidates into nodules and non-nodules depending on their features. As the objective is to find nodules bigger than 4mm, the proposed approach demonstrated quite encouraging results. Among 65 computer tomography (CT scans, 94.23% of sensitivity and 84.75% in specificity were obtained. The accuracy of these two results was 89.19% taking into consideration that 45 scans were used for testing and 20 for training. The rate of false positives was 0.2 per scan.

  6. Usefulness of semiquantitative elastography in predicting malignancy in thyroid nodules.

    Science.gov (United States)

    Franco Uliaque, C; Pardo Berdún, F J; Laborda Herrero, R; Pérez Lórenz, C

    2016-01-01

    To retrospectively review the diagnostic capacity of semiquantitative elastography in differentiating between benign and malignant thyroid nodules. We analyzed 314 thyroid nodules in 295 consecutive patients referred to the endocrinology department for cytological study, studying all by conventional ultrasonography, elastography, and fine-needle aspiration cytology (FNAC). Using a semiquantitative elastography system that portrays tissue stiffness through a color map, we designed our own classification system for thyroid nodules based on their characteristics on elastography. We classified nodules into three groups: predominantly soft, predominantly stiff, and mosaic patterned. We used logistic regression analysis to investigate the relation between elastography and thyroid cancer. We obtained a definite diagnosis of malignancy after surgery in 19 nodules, of which on elastography 8 had the mosaic pattern, 6 were predominantly stiff, and 5 were predominantly soft. We found no significant association between the pattern on elastography and the probability of malignancy in any of the models. According to our study, la probability of malignancy in a thyroid nodule is not related to the findings at elastography. Therefore, semiquantitative elastography as used in this study cannot obviate FNAC. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

  7. Overview and strategic management of subsolid pulmonary nodules.

    Science.gov (United States)

    Godoy, Myrna C B; Naidich, David P

    2012-07-01

    A new classification of lung adenocarcinoma has been proposed recently-the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society classification. Abundant information from recent lung cancer computed tomography (CT) screening programs has increased our understanding of the strong, although imperfect, correlation between histologic findings of lung adenocarcinoma and subsolid pulmonary nodules on CT, including both "pure" ground-glass nodules (GGNs) and "part-solid" GGNs. Moreover, serial CT imaging has demonstrated stepwise progression of these nodules in a subset of patients, characterized by increase in size and density of GGNs and development of a solid component. Given the higher incidence of malignancy and the considerably lower growth rate of subsolid nodules, dedicated standardized guidelines for management of these nodules have been proposed, including long-term (≥3 y) CT follow-up using a low-dose technique. Radiologists should be familiar with the new terminology of lung adenocarcinomas and strategic management of subsolid pulmonary nodules.

  8. Nodulation and mycorrhization of transgenic soybean after glyphosate application

    Directory of Open Access Journals (Sweden)

    Aloisio Freitas Chagas Junior

    2013-12-01

    Full Text Available The sensitivity of nitrogen-fixing bacteria like Bradyrhizobium spp with in relation to glyphosate can be influenced by the concentration of the herbicide. This study aims to evaluate the effects of two formulations of glyphosate, in two application periods, on nodulation and mycorrhization in a soybean of variety RR P98Y11, using greenhouse, in pots with capacity of 4 L with savanna soils. Six treatments were utilized using Roundup Ultra and Roundup Original with one and two applications, witness without herbicide and witness only with mineral nitrogen, in a completely randomized design. Four evaluations were done, every 15 days, to determine the plant height, shoot and root dry weight, number of nodules, nodule dry weigh and mycorrhizae. It was observed an increase on the number of nodules, with the use of Roundup Ultra until 15 days after the first application. After this period, the witness only with inoculants showed a larger number of nodules. Roundup Ultra had positive influences on the dry weight of nodules, regardless the number of applications. There was no influence of glyphosate formulation considering the mycorrhizal colonization.

  9. On the computed tomographic diagnosis of pulmonary nodules

    International Nuclear Information System (INIS)

    Higashi, Yuuichirou

    1988-01-01

    Computed tomography (CT) was used to examine 53 pulmonary nodules which were considered not definitely calcified on plain radiographs or conventional tomograms. An average CT number was calculate for each lesion. For the primary lung cancers, the average CT number was 36 HU with a standard deviation of 6.6 HU, while the benign lesions had the mean CT number of 69 HU, with a standard deviation of 42.8 HU. The mean CT number separating lung malignancies from benign lesions was 78.8 HU. To evaluate the attenuation values within each nodule, iso-CT value map was obtained by using Siemens therapy planning system, MEVAPLAN. Nodules were classified into five categories, Type I to V. All of three nodules classified as Type IV were benign. Iso-CT value map was effective in establishing the benignancy of nodules. The quantitative computed tomographic analysis of pulmonary nodules was evaluated by dual-energy CT. Dual-energy CT has the potential to eliminate the effect of spectral hardening by use of monoenergic images derived from dual-kV data and to separate high CT numbers due to calcium from those due to high density organic material. (author)

  10. Persistent pulmonary subsolid nodules: model-based iterative reconstruction for nodule classification and measurement variability on low-dose CT

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyungjin; Kim, Seong Ho; Lee, Sang Min; Lee, Kyung Hee [Seoul National University College of Medicine, Department of Radiology, Seoul (Korea, Republic of); Seoul National University Medical Research Center, Institute of Radiation Medicine, Seoul (Korea, Republic of); Park, Chang Min; Park, Sang Joon; Goo, Jin Mo [Seoul National University College of Medicine, Department of Radiology, Seoul (Korea, Republic of); Seoul National University Medical Research Center, Institute of Radiation Medicine, Seoul (Korea, Republic of); Seoul National University, Cancer Research Institute, Seoul (Korea, Republic of)

    2014-11-15

    To compare the pulmonary subsolid nodule (SSN) classification agreement and measurement variability between filtered back projection (FBP) and model-based iterative reconstruction (MBIR). Low-dose CTs were reconstructed using FBP and MBIR for 47 patients with 47 SSNs. Two readers independently classified SSNs into pure or part-solid ground-glass nodules, and measured the size of the whole nodule and solid portion twice on both reconstruction algorithms. Nodule classification agreement was analyzed using Cohen's kappa and compared between reconstruction algorithms using McNemar's test. Measurement variability was investigated using Bland-Altman analysis and compared with the paired t-test. Cohen's kappa for inter-reader SSN classification agreement was 0.541-0.662 on FBP and 0.778-0.866 on MBIR. Between the two readers, nodule classification was consistent in 79.8 % (75/94) with FBP and 91.5 % (86/94) with MBIR (p = 0.027). Inter-reader measurement variability range was -5.0-2.1 mm on FBP and -3.3-1.8 mm on MBIR for whole nodule size, and was -6.5-0.9 mm on FBP and -5.5-1.5 mm on MBIR for solid portion size. Inter-reader measurement differences were significantly smaller on MBIR (p = 0.027, whole nodule; p = 0.011, solid portion). MBIR significantly improved SSN classification agreement and reduced measurement variability of both whole nodules and solid portions between readers. (orig.)

  11. Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

    Directory of Open Access Journals (Sweden)

    Irina V Demina

    Full Text Available Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7% could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

  12. Competitive nodulation blocking of cv. Afghanistan pea is related to high levels of nodulation factors made by some strains of Rhizobium leguminosarum bv. viciae

    NARCIS (Netherlands)

    Hogg, B.; Davies, A.E.; Wilson, K.E.; Bisseling, T.; Downie, J.A.

    2002-01-01

    Cultivar Afghanistan peas are resistant to nodulation by many strains of Rhizobium leguminosarum bv. viciae but are nodulated by strain TOM, which carries the host specificity gene nodX. Some strains that lack nodX can inhibit nodulation of cv. Afghanistan by strain TOM. We present evidence that

  13. Cooled microwave ablation of thyroid nodules: Initial experience

    Energy Technology Data Exchange (ETDEWEB)

    Korkusuz, Yücel [Department of Nuclear Medicine, University Hospital Frankfurt (Germany); Mader, Oscar Maximilian, E-mail: info@dzta.de [Department of Nuclear Medicine, University Hospital Frankfurt (Germany); Kromen, Wolfgang [Department of Neuro Radiology University Hospital (Germany); Happel, Christian [Department of Nuclear Medicine, University Hospital Frankfurt (Germany); German Centre for Thermoablation of Thyroid Nodules, University Hospital, Frankfurt (Germany); Ahmad, Shadi [Department of General and Visceral Surgery, Agaplesion Elisabethenstift, Darmstadt (Germany); Gröner, Daniel; Koca, Mithat; Mader, Alexander [Department of Nuclear Medicine, University Hospital Frankfurt (Germany); Grünwald, Frank; Korkusuz, Hüdayi [Department of Nuclear Medicine, University Hospital Frankfurt (Germany); German Centre for Thermoablation of Thyroid Nodules, University Hospital, Frankfurt (Germany)

    2016-11-15

    Highlights: • cMWA is a safe and effective treatment for thyroid nodules. • Ultrasound imaging allows guidance during microwave ablation. • Pain level during cMWA treatment is reduced in comparison to RFA. - Abstract: Objective: To evaluate if internally cooled microwave ablation (cMWA) is a safe and effective method for treatment of benign and malign thyroid nodules. Methods: 9 patients with 11 symptomatic cold benign thyroid nodules and 1 recurrent thyroid carcinoma ranging in volume from 9.1 to 197 ml (mean size 52 ±  57 ml) were treated with cMWA. The mean age of the patients was 59 years. Pain during the treatment was measured on a 10-point scale. Side effects revealed by ultrasound or patients’ complaints were documented. Periablative efficacy was measured 24 h after cMWA as change (Δ) in serum thyreoglobulin (Tg). Nodule elasticity was measured on a 4-point scale, blood circulation and echogenicity on a 3-point scale. Results: All patients tolerated cMWA well. Median pain intensity averaged 2.1 ± 0.8 (range: 1–3). Postablative hematoma was observed in all cases. In no cases ablation led to hoarseness, superficial burns, nodule ruptures, vagal reactions or dysphagia. cMWA lead to a significant decrease of blood circulation, nodule echogenicity and a significant increase of elasticity (Δ  =  1.1  ±  0.33; 0.8  ±  0.4 and 1.1  ±  0.6 points)(p < 0.05). An average increase of 4495 ng/ml Tg was measured (p < 0.05). Conclusions: cMWA is an effective and secure method for treatment of thyroid nodules.

  14. Nódulo de tiroides Thyroid nodule

    Directory of Open Access Journals (Sweden)

    Silvia Elena Turcios Tristá

    2012-12-01

    Full Text Available En los últimos años se ha incrementado la frecuencia diagnóstica del nódulo de tiroides. Un adecuado método clínico y algunos exámenes complementarios, serán los factores a tener en cuenta para definir la naturaleza de la lesión y su funcionalidad. En la actualidad se adicionan nuevos elementos en los estudios por imagen que ayudan a predecir, en alguna medida, el riesgo de malignidad de estas lesiones, y se trata de que el resultado citológico sea más uniforme y orientador. Las conductas se adecuan al tipo de enfermedad tiroidea y a sus riesgos, pero es imprescindible la unión de las especialidades que tienen que ver con la enfermedad nodular tiroidea, para unificar criterios que favorezcan un adecuado y eficiente proceso diagnóstico-terapéutico, que reduzcan los riesgos y los costos que implica la adopción de conductas inadecuadas e innecesarias.In the last few years, the frequency of diagnosis of the thyroid nodule has increased. A correct clinical method and some supplementary tests are the factors to be taken into account to define the nature of lesion and functionality. At present, new elements are added to the imaging studies, which help to predict somehow the risk of malignancy of these lesions, and it is intended to reach a more uniform and guiding cytological result. The behaviors should adapt to the type of thyroid disease and to the risks, but the combination of those specialties that have to do with the nodular thyroid disease is indispensable in order to uniform criteria favoring adequate and efficient diagnostic and therapeutic processes, and reducing the risks and costs of the adoption of inadequate and unnecessary behaviors.

  15. Colonization and nitrogenase activity of Triticum aestivum (cv. Baccross and Mahdavi) to the dual inoculation with Azospirillum brasilense and Rhizobium meliloti plus 2,4-D.

    Science.gov (United States)

    Mehry, Askary; Akbar, Mostajeran; Giti, Emtiazi

    2008-06-15

    The potential enhancement of root colonization and nitrogenase activity of wheat cultivars (Baccross and Mahdavi) was studied with application of two Azospirillum brasilense strains (native and Sp7) co-inoculated with two Rhizobium meliloti strains (native and DSMZ 30135). The results indicated that the colonization was different due to the strains and cultivars of wheat were used. Native A. brasilense colonized wheat root better than Sp7 strain. However, Baccross cv. reacted better with native Azospirillum compared to Mahdavi cv. which reacted better with Sp7. When plants inoculated with dual inoculants (SP7 with standard Rhizobium), the colonization of Azospirillum were increased significantly (from 1.67 x 10(5) to 22 x 10(5) cfu g(-1) FW for Baccras cv. and 3.67 x 10(5) to 26 x 10(5) cfu g(-1) FW for Mahdavi cultivar). When the standard Rhizobium as co-inoculants changed to the native Rhizobium, the colonization of Azospirillum was higher when compared to the single inoculants but was almost the same when compared to the standard Rhizobium. When the standard or native strains of Rhizobium used as single inoculation of wheat roots, the number of Rhizobium in the wheat roots were not changed significantly. However, when plants co-inoculated with Rhizobium and Azospirillum, the colonization of Rhizobium was increased. Co-inoculation of standard strain of R. melilot with A. brasilense Sp7 showed that the colonization of Rhizobium were increased from 0.67 x 10(5) to 21 x 10(5) cfu g(-1) FW for Baccross cv. and 0.33 x 10(5) to 18 x 10(5) cfu g(-1) FW for Mahdavi cv. This behavior was the same when inoculation of Rhizobium was happened with the native one. In dual inoculation, the highest nitrogenase activity was measured in combination of the local strains (native A. brasilense with the native R. meliloti) and the lower one belongs to the combination of standard strains (Sp7 with standard R. meliloti). The difference in nirtogenase activity for different cultivars of

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

    Science.gov (United States)

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

    2015-12-08

    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.

  17. Microsymbiont discrimination mediated by a host-secreted peptide inMedicago truncatula.

    Science.gov (United States)

    Yang, Shengming; Wang, Qi; Fedorova, Elena; Liu, Jinge; Qin, Qiulin; Zheng, Qiaolin; Price, Paul A; Pan, Huairong; Wang, Dong; Griffitts, Joel S; Bisseling, Ton; Zhu, Hongyan

    2017-06-27

    The legume-rhizobial symbiosis results in the formation of root nodules that provide an ecological niche for nitrogen-fixing bacteria. However, plant-bacteria genotypic interactions can lead to wide variation in nitrogen fixation efficiency, and it is not uncommon that a bacterial strain forms functional (Fix + ) nodules on one plant genotype but nonfunctional (Fix - ) nodules on another. Host genetic control of this specificity is unknown. We herein report the cloning of the Medicago truncatula NFS1 gene that regulates the fixation-level incompatibility with the microsymbiont Sinorhizobium meliloti Rm41. We show that NFS1 encodes a nodule-specific cysteine-rich (NCR) peptide. In contrast to the known role of NCR peptides as effectors of endosymbionts' differentiation to nitrogen-fixing bacteroids, we demonstrate that specific NCRs control discrimination against incompatible microsymbionts. NFS1 provokes bacterial cell death and early nodule senescence in an allele-specific and rhizobial strain-specific manner, and its function is dependent on host genetic background.

  18. Thyroid nodule recognition in computed tomography using first order statistics.

    Science.gov (United States)

    Peng, Wenxian; Liu, Chenbin; Xia, Shunren; Shao, Dangdang; Chen, Yihong; Liu, Rui; Zhang, Zhiping

    2017-06-02

    Computed tomography (CT) is one of the popular tools for early detection of thyroid nodule. The pixel intensity of thyroid in CT image is very important information to distinguish nodule from normal thyroid tissue. The pixel intensity in normal thyroid tissues is homogeneous and smooth. In the benign or malignant nodules, the pixel intensity is heterogeneous. Several studies have shown that the first order features in ultrasound image can be used as imaging biomarkers in nodule recognition. In this paper, we investigate the feasibility of utilizing the first order texture features to identify nodule from normal thyroid tissue in CT image. A total of 284 thyroid CT images from 113 patients were collected in this study. We used 150 healthy controlled thyroid CT images from 55 patients and 134 nodule images (50 malignant and 84 benign nodules) from 58 patients who have undergone thyroid surgery. The final diagnosis was confirmed by histopathological examinations. In the presented method, first, regions of interest (ROIs) from axial non-enhancement CT images were delineated manually by a radiologist. Second, average, median, and wiener filter were applied to reduce photon noise before feature extraction. The first-order texture features, including entropy, uniformity, average intensity, standard deviation, kurtosis and skewness were calculated from each ROI. Third, support vector machine analysis was applied for classification. Several statistical values were calculated to evaluate the performance of the presented method, which includes accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area of under receiver operating characteristic curve (AUC). The entropy, uniformity, mean intensity, standard deviation, skewness (P < 0.05), except kurtosis (P = 0.104) of thyroid tissue with nodules have a significant difference from those of normal thyroid tissue. The optimal classification was obtained from the presented

  19. Thyroid Nodules Individual Pathologic Assessment in Imam Reza Hospital Tabriz

    Directory of Open Access Journals (Sweden)

    Saeed Judi

    2017-02-01

    Full Text Available Background and Objectives: Single thyroid nodule is a common clinical finding in patients with thyroid gland enlargment or with palpable mass in anterior neck. Because of various pathologic kinds and wide spectrum of nodules from inflammatory disease to benign and malignan tumors, pathologically diagnosis of disease is very important because treatment, prognosiss and approach will differ with respect to diagnosis. Because of importance and high incidence of disease, we decided to investigate records of patients in pathology department of Imam Reza hospital of Tabriz between 2011-14. Our goals were determination of pathologic incidence of single thyroid nodules and investigation of them by sex and age. After extracting results from records, we presented them in the form of tables and figure. Material and Methods: In total, 17349 patients referred to pathology department of Imam Reza hospital between 2011-14. In 191 cases the first clinical diagnosiss was single thyroid nodule. Thyroids specimes were sent to pathology department. Results: The most common pathologic report was multinodular goiter in 90 patients (47%. Other kinds were follicular adenoma 28%, papillary carcinoma 15%, follicular carcinoma and diffuse goiter 3%, lymphocytic thyroiditis, medulary carcinoma 1%, granuloma, lymphoma and abscess each one 0.5%, respectively. Conclusion: Most cases of thyroid nodules are nodular goiter and it is prevalent among females.

  20. Multicellular contractility contributes to the emergence of mesothelioma nodules

    Science.gov (United States)

    Czirok, Andras

    Malignant pleural mesothelioma (MPM) nodules arise from the mesothelial lining of the pleural cavity by a poorly understood mechanism. We demonstrate that macroscopic multicellular aggregates, reminiscent of the MPM nodules found in patients, develop when MPM cell lines are cultured at high cell densities for several weeks. Surprisingly, the nodule-like aggregates do not arise by excessive local cell proliferation, but by myosin II-driven cell contractility. Contractile nodules contain prominent actin cables that can span several cells. Several features of the in vitro MPM nodule development can be explained by a computational model that assumes uniform and steady intercellular contractile forces within a monolayer of cells, and a mechanical load-dependent lifetime of cell-cell contacts. The model behaves as a self-tensioned Maxwell fluid and exhibits an instability that leads to pattern formation. Altogether, our findings suggest that inhibition of the actomyosin system may provide a hitherto not utilized therapeutic approach to affect MPM growth. NIH R01-GM102801.

  1. Phenolphthalein false-positive reactions from legume root nodules.

    Science.gov (United States)

    Petersen, Daniel; Kovacs, Frank

    2014-03-01

    Presumptive tests for blood play a critical role in the examination of physical evidence and in the determination of subsequent analysis. The catalytic power of hemoglobin allows colorimetric reactions employing phenolphthalein (Kastle-Meyer test) to indicate "whether" blood is present. Consequently, DNA profiles extracted from phenolphthalein-positive stains are presumed to be from blood on the evidentiary item and can lead to the identification of "whose" blood is present. Crushed nodules from a variety of legumes yielded phenolphthalein false-positive reactions that were indistinguishable from true bloodstains both in color quality and in developmental time frame. Clothing and other materials stained by nodules also yielded phenolphthalein false-positive reactivity for several years after nodule exposure. Nodules from leguminous plants contain a protein (leghemoglobin) which is structurally and functionally similar to hemoglobin. Testing of purified leghemoglobin confirmed this protein as a source of phenolphthalein reactivity. A scenario is presented showing how the presence of leghemoglobin from nodule staining can mislead investigators. © 2013 American Academy of Forensic Sciences.

  2. Thyroid nodules with nondiagnostic results on repeat fine-needle aspiration biopsy: which nodules should be considered for repeat biopsy or surgery rather than follow-up?

    Energy Technology Data Exchange (ETDEWEB)

    Eun, Na Lae; Chang, Hang Seok; Gweon, Hye Mi; Kim, Jeong Ah; Youk, Ji Hyun; Son, Eun Jun [Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Yoo, Mi Ri [Dept. of Radiology, Dongjak Kyunghee Hospital, Seoul (Korea, Republic of); Park, Ah Young [Dept. of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, Ansan (Korea, Republic of); Moon, Hee Jung [Dept. of Radiology and Research Institute of Radiological Science, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2016-07-15

    The goal of this study was to assess the clinicopathologic and ultrasonographic features of thyroid nodules with nondiagnostic results on repeat ultrasonography (US)-guided fineneedle aspiration biopsy (FNAB) according to size and the number of suspicious findings and to determine the proper management of nodules with consecutive nondiagnostic results. This retrospective study included 297 nodules with nondiagnostic results on repeat FNAB that were evaluated by US over the course of at least 12 months of follow-up, a follow-up biopsy, or an operation. We compared clinical and US variables between benign and malignant nodules in thyroid nodules with repeat nondiagnostic results. The comparison of benign and malignant nodules with repeat nondiagnostic results revealed that age, marked hypoechogenicity, irregular or microlobulated margins, microcalcifications, and nonparallel shape were significantly associated with malignancy. Multivariate logistic regression analysis in malignant nodules revealed that microcalcifications and irregular or microlobulated margins were independently associated with malignancy. Among them, only irregular or microlobulated margins were independently significant as a predictor of malignancy in repeatedly nondiagnostic nodules measuring >10 mm. Using receiver operating characteristic analysis, the best cutoff value for the “number of suspicious findings” between benign and malignant nodules was three in nodules of all sizes, three in nodules measuring ≤10 mm, and two in nodules measuring >10 mm. Irregular or microlobulated margins may be the most frequent US features in repeatedly nondiagnostic nodules >10 mm. The presence of “two or more suspicious findings” can be used as the cutoff for distinguishing benign and malignant nodules.

  3. Variability of Mn, Fe, Ni, Cu and Co in manganese nodules from the Central Indian Ocean Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Jauhari, P.

    The trace element variations in manganese nodules from the Central Indian Basin have been related to the underlying sediment type. Percentages of Mn, Cu and Ni are high in nodules occurring in siliceous sediments compared with nodules from the red...

  4. Usefulness of the CAD System for Detecting Pulmonary Nodule in Real Clinical Practice

    International Nuclear Information System (INIS)

    Song, Kyoung Doo; Chung, Myung Jin; Kim, Hee Cheol; Lee, Kyung Soo; Jeong, Sun Young

    2011-01-01

    We wanted to evaluate the usefulness of the computer-aided detection (CAD) system for detecting pulmonary nodules in real clinical practice by using the CT images. Our Institutional Review Board approved our retrospective study with a waiver of informed consent. This study included 166 CT examinations that were performed for the evaluation of pulmonary metastasis in 166 patients with colorectal cancer. All the CT examinations were interpreted by radiologists and they were also evaluated by the CAD system. All the nodules detected by the CAD system were evaluated with regard to whether or not they were true nodules, and they were classified into micro nodules (MN, diameter < 4 mm) and significant nodules (SN, 4 ≤ diameter ≤ 10 mm). The radiologic reports and CAD results were compared. The CAD system helped detect 426 nodules: 115 (27%) of the 426 nodules were classified as true nodules and 35 (30%) of the 115 nodules were SNs, and 83 (72%) of the 115 were not mentioned in the radiologists' reports and three (4%) of the 83 nodules were non-calcified SNs. One of three non-calcified SNs was confirmed as a metastatic nodule. According to the radiologists' reports, 60 true nodules were detected, and 28 of the 60 were not detected by the CAD system. Although the CAD system missed many SNs that are detected by radiologists, it helps detect additional nodules that are missed by the radiologists in real clinical practice. Therefore, the CAD system can be useful to support a radiologist's detection performance

  5. Prognosis of thyroid nodules in individuals living in the Zhitomir region of Ukraine.

    Directory of Open Access Journals (Sweden)

    Naomi Hayashida

    Full Text Available 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.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.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.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.

  6. Mucoid impaction presenting as multiple pulmonary nodules in cystic fibrosis

    International Nuclear Information System (INIS)

    Carpenter, L.D.; Lambie, N.K.; Wilsher, M.L.

    1996-01-01

    Mucoid impaction has been described as a complication of asthma and more commonly in patients with allergic bronchopulmonary aspergillosis. In such cases, the impacted pools of mucus may present as discrete nodules on chest X-ray and hence simulate the appearance of metastatic malignancy. A case of mucoid impaction presenting as multiple pulmonary nodules in a patient with cystic fibrosis is described. The chest X-ray showed hyperinfiltration and scattered changes consistent with bronchiectasis. Computed tomography scan confirmed these and additional intra-pulmonary nodular densities. This report illustrates that mucus impaction as a cause of pulmonary nodules should be considered in any patient with chronic lung disease characterised by excess mucus production. 6 refs., 3 figs

  7. Nonsurgical, image-guided, minimally invasive therapy for thyroid nodules

    DEFF Research Database (Denmark)

    Gharib, Hossein; Hegedüs, Laszlo; Pacella, Claudio Maurizio

    2013-01-01

    Context: Nodular thyroid disease is very common. Most nodules are asymptomatic, are benign by fine-needle aspiration, remain stable, and can be followed by observation alone in the majority of the patients. Occasionally, nodules grow or cause symptoms requiring treatment. So far, surgery has been...... our main option for treatment. Objective: In this review, we discuss nonsurgical, minimally invasive approaches for small thyroid masses, including indications, efficacy, side effects, and costs. Evidence Acquisition: We selected recent publications related to minimally invasive thyroid techniques...... therapy is recommended for recurrent benign thyroid cysts. Either ultrasound-guided laser or radiofrequency ablation can be used for symptomatic solid nodules with normal or abnormal thyroid function. Microwave ablation and high-intensity focused ultrasound are newer approaches that need further clinical...

  8. Malignancy risk estimation of pulmonary nodules in screening CTs

    DEFF Research Database (Denmark)

    van Riel, Sarah J; Ciompi, Francesco; Winkler Wille, Mathilde M

    2017-01-01

    PURPOSE: To compare human observers to a mathematically derived computer model for differentiation between malignant and benign pulmonary nodules detected on baseline screening computed tomography (CT) scans. METHODS: A case-cohort study design was chosen. The study group consisted of 300 chest CT...... scans from the Danish Lung Cancer Screening Trial (DLCST). It included all scans with proven malignancies (n = 62) and two subsets of randomly selected baseline scans with benign nodules of all sizes (n = 120) and matched in size to the cancers, respectively (n = 118). Eleven observers and the computer....... Differences in morphological features between malignant and size-matched benign nodules were analyzed using chi-square analysis with Bonferroni correction. A significant difference was defined at p

  9. Solitary pulmonary nodule by pulmonary hematoma under warfarin therapy

    International Nuclear Information System (INIS)

    Scheppach, W.; Kulke, H.; Liebau, G.; Braun, H.; Wuerzburg Univ.

    1983-01-01

    Pulmonary hematoma is a rare cause of a pulmonary nodule. Mostly it results from penetrating or blunt chest injuries. The case of a patient is reported, whose chest X-ray showed a pulmonary nodule suspected of malignancy. This patient was maintained permanently on anticoagulants (warfarin derivates) after cardiac valve replacement with a prosthesis. A definite diagnosis could not be established by non-invasive methods. A needle biopsy of the lung was impracticable because of the location of the pulmonary lesion; an exploratory thoracotomy could not be carried out due to a general indication of nonoperability. Control examinations showed that the pulmonary nodule had vanished completely within four months. In consideration of the patient's clinical situation it can be concluded that the pulmonary lesion was caused by a hematoma of the lung. (orig.) [de

  10. Undercooling and nodule count in thin walled ductile iron castings

    DEFF Research Database (Denmark)

    Pedersen, Karl Martin; Tiedje, Niels Skat

    2007-01-01

    Casting experiments have been performed with eutectic and hypereutectic castings with plate thick¬nesses from 2 to 8 mm involving both temperature measurements during solidification and micro¬structural examination afterwards. The nodule count was the same for the eutectic and hypereutectic...... castings in the thin plates ( 4.3 mm) while in the 8 mm plate the nodule count was higher in the hypereutectic than in the eutectic castings. The minimum temperature prior to the eutectic recalescence (Tmin) was 15 to 20C lower for the eutectic than the hypereutectic castings. This is due to nucleation...... of graphite nodules which begins at a lover temperature in the eutectic than in the hypereutectic castings The recalescence (Trec) was however also larger for the eutectic casting and in the thin plates the maximum temperature after recalescence (Tmax) was the same in the eutectic and hypereutectic plates...

  11. Electrochemical polarization studies of nodulation phenomenon during copper electrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Lafront, A-M.; Veilleux, B.; Ghali, E. [Laval Univ., Dept. of Mining, Metallurgy and Material Engineering, Sainte-Foy, Quebec (Canada)

    2001-07-01

    The use of thiourea, gelatin and chloride additives during copper electrorefining promotes smooth cathode deposits, but inappropriate additive concentrations and/or molar ratios can lead to nodule formation, when operating at current densities slightly higher than 300 A/m{sup 2} and at 65{sup o}C. In voltammograms at potential sweep rates of 0.05 mV/s, a limiting current density was observed for a cathode potential range of the order of 50 mV. Galvanostatic polarization measurements followed by microscopic examination proved this to be related to nodule formation. A diagram was conceived to delineate current densities for nodule-free copper deposit as functions of the concentrations and molar ratios of the additives. (author)

  12. Transcription of the soybean leghemoglobin genes during nodule development

    DEFF Research Database (Denmark)

    Marcker, Anne; Lund, Marianne; Jensen, Erik Ø

    1984-01-01

    During the early stages of soybean nodule development the leghemoglobin (Lb) genes are activated sequentially in the opposite order to which they are arranged in the soybean genome. At a specific stage after the initial activation of all the Lb genes, a large increment occurs in the transcription...... of the Lb(c1), Lb(c3) and Lb(a) genes while the transcription of the Lb(c2) gene is not amplified to a similar extent. All the Lb genes retain significant activity for a long period during the lifetime of a nodule. Consequently the soybean Lb genes are not regulated by a developmental gene switching...... mechanism as is the case for vertebrate globin genes. Concomitantly with the increase in Lb gene transcription some of the other nodule specific plant genes are activated. These specific changes in the activities of the Lb and nodulin genes precede the activation of the bacterial nitrogenase gene. Thus...

  13. Undercooling and nodule count in thin walled ductile iron castings

    DEFF Research Database (Denmark)

    Pedersen, Karl Martin; Tiedje, Niels Skat

    2007-01-01

    Casting experiments have been performed with eutectic and hypereutectic castings with plate thicknesses from 2 to 8 mm involving both temperature measurements during solidification and microstructural examination afterwards. The nodule count was the same for the eutectic and hypereutectic castings...... in the thin plates (≤4.3 mm) while in the 8 mm plate the nodule count was higher in the hypereutectic than in the eutectic castings. The minimum temperature before the eutectic recalescence (Tmin) was 15 to 20ºC lower for the eutectic than for the hypereutectic castings. This is due to nucleation of graphite...... nodules which begins at a lower temperature in the eutectic than in the hypereutectic castings. The recalescence ∆Trec was however also larger for the eutectic casting and in the thin plates the maximum temperature after recalescence (Tmax) was the same in the eutectic and hypereutectic plates...

  14. Lung Nodule Detection in CT Images using Neuro Fuzzy Classifier

    Directory of Open Access Journals (Sweden)

    M. Usman Akram

    2013-07-01

    Full Text Available Automated lung cancer detection using computer aided diagnosis (CAD is an important area in clinical applications. As the manual nodule detection is very time consuming and costly so computerized systems can be helpful for this purpose. In this paper, we propose a computerized system for lung nodule detection in CT scan images. The automated system consists of two stages i.e. lung segmentation and enhancement, feature extraction and classification. The segmentation process will result in separating lung tissue from rest of the image, and only the lung tissues under examination are considered as candidate regions for detecting malignant nodules in lung portion. A feature vector for possible abnormal regions is calculated and regions are classified using neuro fuzzy classifier. It is a fully automatic system that does not require any manual intervention and experimental results show the validity of our system.

  15. Studies on zinc nodules electrodeposited from acid electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Rolfe [Univ. of California, Berkeley, CA (United States); Tobias, Charles W. [Univ. of California, Berkeley, CA (United States)

    1984-12-01

    The development of morphology of electrodeposited zinc was investigated by studying the initial stages of deposition. Zinc was deposited galvanostatically from 1.0 M ZnCl2 electrolyte (0.7 < pH < 4.6) on rotating disc electrodes at current densities from 5 to 130 ma/cm2. Pine glassy carbon, Union Carbide pyrolytic graphite, Gould pyrolytic graphite, Exxon graphite loaded polymer, and platinum substrates were used. The number densities of nodules (diameter greater than 1 μm), typically encountered during incipient morphological development, were measured using scanning electron microscopy and image analysis. Nodule densities up to 7 x 104 nodules/mm2 were measured.

  16. Persistent Scabious Nodules (A Clinico-pathologic Study

    Directory of Open Access Journals (Sweden)

    Vinod K Sharma

    1986-01-01

    Full Text Available Twenty-nine (5.33% out of 544 patients of scabies had persistent smbious nodules. Young adults (16-30 years and children under 15 years constituted 48.27% and 34.48% patients respectively. All but one were males, scrotum (96.55% and penis (69.0% were the commonest sites affected, followed by axillaiy region (37.93% and groins (17.24%. Nodules disappeared in all the patients within 4 months. Histopathlogical studies done in 11 patients showed intracellular or intercellular oedema, occasionally distinct vesicle formation and focal or dif fuse infiltrate by lymphomononuclear cells, plasma cells and eosinophils.

  17. Desmoid tumor of bone with enchondromatous nodules, mistaken for chondrosarcoma

    Energy Technology Data Exchange (ETDEWEB)

    Bahk, Won-Jong [Musculoskeletal Oncology Study Group, Catholic University of Korea (Korea); Department of Orthopaedic Surgery, Uijongbu St. Mary' s Hospital, 65-1 Geumohdong, Uijongbu, Gyunggido, 480-130 (Korea); Kang, Yong-Koo; Lee, An-Hee [Musculoskeletal Oncology Study Group, Catholic University of Korea (Korea); Mirra, Joseph M. [Orthpaedic Oncology, Orthopaedic Hospital, Los Angeles, CA (United States)

    2003-04-01

    Desmoid tumor of bone, also termed desmoplastic fibroma or aggressive fibromatosis, is a rare, locally aggressive fibroblastic tumor. We present a 16-year-old male with a huge desmoid tumor involving the iliac wing. It was associated with enchondromatous nodules mimicking malignancy. The tumor in this patient was mistaken for chondrosarcoma and hemipelvectomy was performed. To our knowledge, such a case has not previously been documented fully in the English literature. The radiographic and pathologic findings and a possible mechanism of enchondromatous nodule formation in fibrous bone tumors are discussed. (orig.)

  18. Cervical Paraganglioma Mimicking Thyroid Nodule: A Rare Clinical Case

    Directory of Open Access Journals (Sweden)

    Berna İmge Aydoğan

    2016-01-01

    Full Text Available Objective. Paraganglioma is a rare neuroendocrine tumor. When it is located in the neck, it is commonly misdiagnosed as other thyroid neoplasms. Case Report. We report a case of cervical paraganglioma in a 55-year-old female. Patient was admitted to our clinic with goiter and neck pain. Thyroid ultrasonography revealed a 20 mm solitary, heterogeneous nodule located in the upper pole of left thyroid lobe. Fine needle aspiration cytology was nondiagnostic. She underwent left lobectomy and histopathology showed paraganglioma. Discussion. Cervical paragangliomas should be considered in the differential diagnosis of thyroid nodules.

  19. NAA of two deep sea manganese nodule RMs for multielements

    International Nuclear Information System (INIS)

    Ni Bangfa; Tian Weizhi; Wang Pingsheng; Yu Zhanqin

    2002-01-01

    Mn-nodule is one of the most important deep sea mineral resources to be explored and exploited in the next century. Analytical quality control based on these kinds of CRMs is therefore necessary. In present work, nearly 30 elements in two Chinese Mn nodule RMs, GSPN-2 and GSPN-3, were determined using extended K 0 -relative comparison NAA technique, developed in our laboratory. The unique features of this work include: i) high accuracy obtained by the internal-validation function of our technique; ii) extensive determinable elements obtained by the hybrid nature of our software; and iii) neutron flux self-shielding corrections. (author)

  20. NAA of two deep sea manganese nodule RMs for multielements

    International Nuclear Information System (INIS)

    Bangfa Ni; Zhanqin Yu; Gaokui He; Pingsheng Wang; Weizhi Tian

    1997-01-01

    Mn-nodule is one of the most important deep sea mineral resources to be explored and exploited in the next century. Analytical quality control based on this kind of Certified Reference Materials (CRMs) is therefore necessary. In the present work, nearly 30 elements in two Chinese Mn nodule Reference Materials (RMs), GSPN-2 and GSPN-3, were determined using extended K 0 -relative comparison NAA technique, developed in our laboratory. The unique features of this work include: (1) high accuracy obtained by the internal validation function of our technique; (2) extensive determinable elements obtained by the hybrid nature of our software and (3) neutron flux self-shielding corrections. (author)

  1. Anatomy and ultrastructure of root nodules of Lupinus luteus

    Directory of Open Access Journals (Sweden)

    A. Woźny

    2015-01-01

    Full Text Available The paper presents anatomic structure of root nodules of lupine (Lupinus luteus L. cv. Express and ultrastructure of cells infected by Rhizobium, The inside of cells from the infected nodule region was filled with numerous bacteria; only centrally located cell nucleus was free of bacteria. Rhizobium was present mostly in the form of "transforming bacteria" (according to the terminology by Ching et al. 1977, characterized by visible nucleoid areas, numerous ribosomes, and polyphosphate granules, although typical bacterioids with poly-β-hydroxybutyrate were also found.

  2. Transcription of the soybean leghemoglobin genes during nodule development

    DEFF Research Database (Denmark)

    Marcker, Anne; Ø Jensen, Erik; Marcker, Kjeld A

    1984-01-01

    During the early stages of soybean nodule development the leghemoglobin (Lb) genes are activated sequentially in the opposite order to which they are arranged in the soybean genome. At a specific stage after the initial activation of all the Lb genes, a large increment occurs in the transcription...... of the Lb(c1), Lb(c3) and Lb(a) genes while the transcription of the Lb(c2) gene is not amplified to a similar extent. All the Lb genes retain significant activity for a long period during the lifetime of a nodule. Consequently the soybean Lb genes are not regulated by a developmental gene switching...

  3. A lung cancer case with numerous calcified metastatic nodules of the brain

    International Nuclear Information System (INIS)

    Fukuda, Y.; Homma, T.; Kohga, H.; Uki, J.; Shisa, H.

    1988-01-01

    A case of pulmonary adenocarcinoma with numerous calcified metastatic nodules of the brain is reported. Autopsy revealed about 400 metastatic nodules in the central nervous system, most of which were calcified. (orig.)

  4. Mineralogy and chemistry of manganese nodules from the Southern part of Carlsberg Ridge

    Digital Repository Service at National Institute of Oceanography (India)

    Karisiddaiah, S.M.

    Petrographic study indicates that the nucleus of nodules is generally composed of clay, volcanic glass, basalt fragments, and earlier nodules. polished sections indicate typical collomorphic globular segregations and partly crystalline oxides...

  5. Underwater geomorphology as a function of the variations in ferromanganese nodule characters in the Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Mukhopadhyay, R.; Banerjee, G.

    Ferromanganese nodules from three areas in the northern part of the Central Indian Ocean Basin have been studied. Statistical analysis shows significant variations in morphological and physical characters of nodules between the area S sub(5), which...

  6. Ore grade manganese nodules from the central Indian basin: an evaluation

    Digital Repository Service at National Institute of Oceanography (India)

    Sudhakar, M.

    processes. The results indicate that the nodules from siliceous sediments approximate the diagenetic end members of the series, as described in the Pacific, and are similar in composition to the north equatorial Pacific ore grade nodules. Siliceous sediments...

  7. Internal constitution of manganese nodules from the Central Indian Ocean basin

    Digital Repository Service at National Institute of Oceanography (India)

    Ghosh, A.K.; Mukhopadhyay, R.

    Morphological, chemical, physical and acoustic properties of Mn-nodules in the the Indian Ocean are inter-linked and depend much on local and regional oceanic environments. These nodules are anisotropic and sound propagation is faster parallel...

  8. Evidence for the formation of different-sized nodules by different accretionary processes

    Digital Repository Service at National Institute of Oceanography (India)

    Valsangkar, A.B.; Karisiddaiah, S.M.

    . S and I type nodule are more abundant than B, L, and V types. Nodules grouped according to their size have common morphological, mineralogical, and geochemical characteristics and all six groups have distinguishing properties. There is evidence which...

  9. Magnesium-content of Rhizobium nodules in different plants: the importance of magnesium in nitrogen-fixation of nodules.

    Science.gov (United States)

    Kiss, Sandor A; Stefanovits-Bányai, Eva; Takács-Hájos, Maria

    2004-12-01

    Rhizobium bacteria induce nodules (tumors) in roots of leguminous crops that fix nitrogen (N2) from the atmosphere. Trials were carried on in sterile perlite where two species of peas were grown hydroponically, and in two different soil types (brown forest soil and meadow silt soil), in a field where different leguminous plants were chosen for test plants: lupin, soybean, broad-bean, lentil and bean inoculated by Rhizobium bacteria. The Mg-content of the nutrient solution was higher than that of the control, but in the soil tests 1% Mg leaf fertilization was applied after bacterial inoculation. Number, weight and Mg-content of nodules were evaluated using an AAS method compared with the thick and thin hair/roots of the given plant. Our results clearly show that the Mg nutrition treatment increased the number of Rhizobium nodules and their Mg-content, resulting in increased N2-fixation and yield.

  10. Competitive nodulation blocking of cv. Afghanistan pea is related to high levels of nodulation factors made by some strains of Rhizobium leguminosarum bv. viciae.

    Science.gov (United States)

    Hogg, Bridget; Davies, Andrea E; Wilson, Karen E; Bisseling, Ton; Downie, J Allan

    2002-01-01

    Cultivar Afghanistan peas are resistant to nodulation by many strains of Rhizobium leguminosarum bv. viciae but are nodulated by strain TOM, which carries the host specificity gene nodX. Some strains that lack nodX can inhibit nodulation of cv. Afghanistan by strain TOM. We present evidence that this "competitive nodulation-blocking" (Cnb) phenotype may result from high levels of Nod factors inhibiting nodulation of cv. Afghanistan peas. The TOM nod gene region (including nodX) is cloned on pIJ1095, and strains (including TOM itself) carrying pIJ1095 nodulate cv. Afghanistan peas very poorly but can nodulate other varieties normally. The presence of pIJ1095, which causes increased levels of Nod factor production, correlates with Cnb. Nodulation of cv. Afghanistan by TOM is also inhibited by a cloned nodD gene that increases nod gene expression and Nod factor production. Nodulation of cv. Afghanistan can be stimulated if nodD on pIJ1095 is mutated, thus severely reducing the level of Nod factor produced. Repression of nod gene expression by nolR eliminates the Cnb phenotype and can stimulate nodulation of cv. Afghanistan. Addition of Nod factors to cv. Afghanistan roots strongly inhibits nodulation. The Cnb+ strains and added Nod factors inhibit infection thread initiation by strain TOM. The sym2A allele determines resistance of cv. Afghanistan to nodulation by strains of R. leguminosarum bv. viciae lacking nodX. We tested whether sym2A is involved in Cnb by using a pea line carrying the sym2A region introgressed from cv. Afghanistan; nodulation in the introgressed line was inhibited by Cnb+ strains. Therefore, the sym2A region has an effect on Cnb, although another locus (or loci) may contribute to the stronger Cnb seen in cv. Afghanistan.

  11. Evaluation of an improved method of simulating lung nodules in chest tomosynthesis

    International Nuclear Information System (INIS)

    Svalkvist, Angelica; Allansdotter Johnsson, Aase; Vikgren, Jenny

    2012-01-01

    Background Simulated pathology is a valuable complement to clinical images in studies aiming at evaluating an imaging technique. In order for a study using simulated pathology to be valid, it is important that the simulated pathology in a realistic way reflect the characteristics of real pathology. Purpose To perform a thorough evaluation of a nodule simulation method for chest tomosynthesis, comparing the detection rate and appearance of the artificial nodules with those of real nodules in an observer performance experiment. Material and Methods A cohort consisting of 64 patients, 38 patients with a total of 129 identified pulmonary nodules and 26 patients without identified pulmonary nodules, was used in the study. Simulated nodules, matching the real clinically found pulmonary nodules by size, attenuation, and location, were created and randomly inserted into the tomosynthesis section images of the patients. Three thoracic radiologists and one radiology resident reviewed the images in an observer performance study divided into two parts. The first part included nodule detection and the second part included rating of the visual appearance of the nodules. The results were evaluated using a modified receiver-operating characteristic (ROC) analysis. Results The sensitivities for real and simulated nodules were comparable, as the area under the modified ROC curve (AUC) was close to 0.5 for all observers (range, 0.43-0.55). Even though the ratings of visual appearance for real and simulated nodules overlapped considerably, the statistical analysis revealed that the observers to were able to separate simulated nodules from real nodules (AUC values range 0.70-0.74). Conclusion The simulation method can be used to create artificial lung nodules that have similar detectability as real nodules in chest tomosynthesis, although experienced thoracic radiologists may be able to distinguish them from real nodules

  12. Inflammatory Hepatic Nodules Associated with Urinary Tract Infection in Two Pediatric Patients

    International Nuclear Information System (INIS)

    Kim, Ye Lim; Kim, Kyeong Ah; Lee, Chang Hee; Choi, Jae Woong; Lee, Jong Mee; Park, Cheol Min

    2009-01-01

    Inflammatory nodule in the liver associated with acute urinary infection is an uncommon presentation. We recently experienced two pediatric patients, admitted for urinary tract infection, in whom a solitary hyperechoic nodule or multiple low echoic nodules in the liver were incidentally discovered. All patients complained of fever, and urine culture results were positive for Klebsiella, Streptococcus, and Escherichia coli. After receiving treatment with antibiotics, the hepatic nodules gradually decreased in size and completely disappeared

  13. Inflammatory Hepatic Nodules Associated with Urinary Tract Infection in Two Pediatric Patients

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ye Lim; Kim, Kyeong Ah; Lee, Chang Hee; Choi, Jae Woong; Lee, Jong Mee; Park, Cheol Min [Korea University Guro Hospital, Korea University College of Medicine, Seoul (Korea, Republic of)

    2009-12-15

    Inflammatory nodule in the liver associated with acute urinary infection is an uncommon presentation. We recently experienced two pediatric patients, admitted for urinary tract infection, in whom a solitary hyperechoic nodule or multiple low echoic nodules in the liver were incidentally discovered. All patients complained of fever, and urine culture results were positive for Klebsiella, Streptococcus, and Escherichia coli. After receiving treatment with antibiotics, the hepatic nodules gradually decreased in size and completely disappeared

  14. Thyroid Nodule Size at Ultrasound as a Predictor of Malignancy and Final Pathologic Size.

    Science.gov (United States)

    Cavallo, Allison; Johnson, Daniel N; White, Michael G; Siddiqui, Saaduddin; Antic, Tatjana; Mathew, Melvy; Grogan, Raymon H; Angelos, Peter; Kaplan, Edwin L; Cipriani, Nicole A

    2017-05-01

    Thyroid-related mortality has remained constant despite the increasing incidence of thyroid carcinoma. Most thyroid nodules are benign; therefore, ultrasound and fine needle aspiration (FNA) are integral in cancer screening. We hypothesize that increased nodule size at ultrasound does not predict malignancy and correlation between nodule size at ultrasound and pathologic exam is good. Resected thyroids with preoperative ultrasounds were identified. Nodule size at ultrasound, FNA diagnosis by Bethesda category, size at pathologic examination, and final histologic diagnosis were recorded. Nodule characteristics at ultrasound and FNA diagnoses were correlated with gross characteristics and histologic diagnoses. Nodules for which correlation could not be established were excluded. Of 1003 nodules from 659 patients, 26% were malignant. Nodules 6 cm). At ultrasound size cutoffs of 2, 3, 4, and 5 cm, smaller nodules had higher malignancy rates than larger nodules. Of the 455 not subject to FNA, 11% were malignant. Ultrasound size alone is a poor predictor of malignancy, but a relatively good predictor of final pathologic size (R 2  = 0.748), with less correlation at larger sizes. In nodules subject to FNA, false negative diagnoses were highest (6-8%) in nodules 3-6 cm, mostly due to encapsulated follicular variant of papillary carcinoma. Thyroid nodule size is inversely related to malignancy risk, as larger nodules have lower malignancy rates. However, the relationship of size to malignancy varies by FNA status. All nodules (regardless of FNA status) demonstrate a risk trough at ≥2 cm. Nodules subject to FNA show step-wise decline in malignancy rates by size, demonstrating that size alone should not be considered as an independent risk factor. Size at ultrasound shows relatively good correlation with final pathologic size. False negative rates are low in this series. Lesions with the appropriate constellation of clinical and radiographic findings should

  15. Interstitial laser photocoagulation (ILP) of benign cystic thyroid nodules--a prospective randomized trial

    DEFF Research Database (Denmark)

    Døssing, Helle; Bennedbæk, Finn Noe; Hegedüs, Laszlo

    2013-01-01

    Recurrence rate, after aspiration, in cystic thyroid nodules is very high. Interstitial laser photocoagulation (ILP) is a minimally invasive procedure that reduces the need for surgery in patients with a benign solid thyroid nodule.......Recurrence rate, after aspiration, in cystic thyroid nodules is very high. Interstitial laser photocoagulation (ILP) is a minimally invasive procedure that reduces the need for surgery in patients with a benign solid thyroid nodule....

  16. Balance the nodule shape and surroundings: a new multichannel image based convolutional neural network scheme on lung nodule diagnosis

    Science.gov (United States)

    Sun, Wenqing; Zheng, Bin; Huang, Xia; Qian, Wei

    2017-03-01

    Deep learning is a trending promising method in medical image analysis area, but how to efficiently prepare the input image for the deep learning algorithms remains a challenge. In this paper, we introduced a novel artificial multichannel region of interest (ROI) generation procedure for convolutional neural networks (CNN). From LIDC database, we collected 54880 benign nodule samples and 59848 malignant nodule samples based on the radiologists' annotations. The proposed CNN consists of three pairs of convolutional layers and two fully connected layers. For each original ROI, two new ROIs were generated: one contains the segmented nodule which highlighted the nodule shape, and the other one contains the gradient of the original ROI which highlighted the textures. By combining the three channel images into a pseudo color ROI, the CNN was trained and tested on the new multichannel ROIs (multichannel ROI II). For the comparison, we generated another type of multichannel image by replacing the gradient image channel with a ROI contains whitened background region (multichannel ROI I). With the 5-fold cross validation evaluation method, the CNN using multichannel ROI II achieved the ROI based area under the curve (AUC) of 0.8823+/-0.0177, compared to the AUC of 0.8484+/-0.0204 generated by the original ROI. By calculating the average of ROI scores from one nodule, the lesion based AUC using multichannel ROI was 0.8793+/-0.0210. By comparing the convolved features maps from CNN using different types of ROIs, it can be noted that multichannel ROI II contains more accurate nodule shapes and surrounding textures.

  17. In situ localization of chalcone synthase mRNA in pea root nodule development.

    NARCIS (Netherlands)

    Yang, W.C.; Canter Cremers, H.C.J.; Hogendijk, P.; Katinakis, P.; Wijffelman, C.A.; Franssen, H.J.; Kammen, van A.; Bisseling, T.

    1992-01-01

    In this paper studies on the role of flavonoids in pea root nodule development are reported. Flavonoid synthesis was followed by localizing chalcone synthase (CHS) mRNA in infected pea roots and in root nodules. In a nodule primordium, CHS mRNA is present in all cells of the primordium. Therefore it

  18. Morphological variations in the polymetallic nodules from selected stations in the Central Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Mukhopadhyay, R.

    Polymetallic nodules from the Central Indian Ocean largely range in size from 2 to 6 cm. The smaller nodules (4 cm) are subspheroidal to spheroidal in shape and with the increase in size, nodules become more discoidal and elongated. The size...

  19. Designing a new CAD system for pulmonary nodule detection in High Resolution Computed Tomography (HRCT images

    Directory of Open Access Journals (Sweden)

    Parsa Hosseini M

    2012-07-01

    Conclusion: Considering the complexity and different shapes of lung nodules and large number of CT images to evaluate, finding lung nodules are difficult and time consuming for physicians and include human error. Experimental results showed the accuracy of the proposed method to be appropriate (P<0.05 for lung nodule detection.

  20. Study of phenanthrene utilizing bacterial consortia associated with cowpea (Vigna unguiculata) root nodules.

    Science.gov (United States)

    Sun, Ran; Crowley, David E; Wei, Gehong

    2015-02-01

    Many legumes have been selected as model plants to degrade organic contaminants with their special associated rhizosphere microbes in soil. However, the function of root nodules during microbe-assisted phytoremediation is not clear. A pot study was conducted to examine phenanthrene (PHE) utilizing bacteria associated with root nodules and the effects of cowpea root nodules on phytoremediation in two different types of soils (freshly contaminated soil and aged contaminated soil). Cowpea nodules in freshly-contaminated soil showed less damage in comparison to the aged-contaminated soil, both morphologically and ultra-structurally by scanning electron microscopy. The study of polycyclic aromatic hydrocarbon (PAH) attenuation conducted by high performance liquid chromatography revealed that more PAH was eliminated from liquid culture around nodulated roots than nodule-free roots. PAH sublimation and denaturation gradient gel electrophoresis were applied to analyze the capability and diversity of PAH degrading bacteria from the following four parts of rhizo-microzone: bulk soil, root surface, nodule surface and nodule inside. The results indicated that the surface and inside of cowpea root nodules were colonized with bacterial consortia that utilized PHE. Our results demonstrated that root nodules not only fixed nitrogen, but also enriched PAH-utilizing microorganisms both inside and outside of the nodules. Legume nodules may have biotechnological values for PAH degradation.

  1. The influence of inspiratory effort and emphysema on pulmonary nodule volumetry reproducibility.

    Science.gov (United States)

    Moser, J B; Mak, S M; McNulty, W H; Padley, S; Nair, A; Shah, P L; Devaraj, A

    2017-11-01

    To evaluate the impact of inspiratory effort and emphysema on reproducibility of pulmonary nodule volumetry. Eighty-eight nodules in 24 patients with emphysema were studied retrospectively. All patients had undergone volumetric inspiratory and end-expiratory thoracic computed tomography (CT) for consideration of bronchoscopic lung volume reduction. Inspiratory and expiratory nodule volumes were measured using commercially available software. Local emphysema extent was established by analysing a segmentation area extended circumferentially around each nodule (quantified as percent of lung with density of -950 HU or less). Lung volumes were established using the same software. Differences in inspiratory and expiratory nodule volumes were illustrated using the Bland-Altman test. The influences of percentage reduction in lung volume at expiration, local emphysema extent, and nodule size on nodule volume variability were tested with multiple linear regression. The majority of nodules (59/88 [67%]) showed an increased volume at expiration. Mean difference in nodule volume between expiration and inspiration was +7.5% (95% confidence interval: -24.1, 39.1%). No relationships were demonstrated between nodule volume variability and emphysema extent, degree of expiration, or nodule size. Expiration causes a modest increase in volumetry-derived nodule volumes; however, the effect is unpredictable. Local emphysema extent had no significant effect on volume variability in the present cohort. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  2. Nonphotosynthetic CO2 fixation by alfalfa (Medicago sativa L.) roots and nodules

    International Nuclear Information System (INIS)

    Anderson, M.P.; Heichel, G.H.; Vance, C.P.

    1987-01-01

    The dependence of alfalfa (Medicago sativa L.) root and nodule nonphotosynthetic CO 2 fixation on the supply of currently produced photosynthate and nodule nitrogenase activity was examined a various times after phloem-girdling and exposure of nodules to Ar:O 2 . Phloem-girdling was effected 20 hours and exposure to Ar:O 2 was effected 2 to 3 hours before initiation of experiments. Nodule and root CO 2 fixation rates of phloem-girdled plants were reduced to 38 and 50%, respectively, of those of control plants. Exposure to Ar:O 2 decreased nodule CO 2 fixation rates to 45%, respiration rates to 55%, and nitrogenase activities to 51% of those of the controls. The products of nodule CO 2 fixation were exported through the xylem to the shoot mainly as amino acids within 30 to 60 minutes after exposure to 14 CO 2 . In contrast to nodules, roots exported very little radioactivity, and most of the 14 C was exported as organic acids. The nonphotosynthetic CO 2 fixation rate of roots and nodules averaged 26% of the gross respiration rate, i.e. the sum of net respiration and nonphotosynthetic CO 2 assimilation. Nodules fixed CO 2 at a rate 5.6 times that of roots, but since nodules comprised a small portion of root system mass, roots accounted for 76% of the nodulated roots system CO 2 fixation. The results indicate that nodule CO 2 fixation in alfalfa is associated with N assimilation

  3. Nodulation and nitrogen fixation of field grown common bean ...

    African Journals Online (AJOL)

    A field experiment was conducted at Bel Air station, in Dakar using 15N isotope dilution technique and the non nodulating soybean (Glycine max) variety m129 as reference plant to test the compatibility of Dichlorofenthion-thiram (DCT) fungicide to the inoculation of common bean (Phaseolus vulgaris) Paulista variety with ...

  4. Thyroglobulin Gene Mutation with Cold Nodule on Thyroid Scintigraphy

    Directory of Open Access Journals (Sweden)

    Toshio Kahara

    2012-01-01

    Full Text Available Thyroglobulin gene mutation is a rare cause of congenital hypothyroidism, but thyroglobulin gene mutations are thought to be associated with thyroid cancer development. A 21-year-old Japanese man treated with levothyroxine for congenital hypothyroidism had an enlarged thyroid gland with undetectable serum thyroglobulin despite elevated serum TSH level. The patient was diagnosed with thyroglobulin gene mutation, with compound heterozygosity for Gly304Cys missense mutation and Arg432X nonsense mutation. Ultrasonography showed a hypovascular large tumor in the left lobe that appeared as a cold nodule on thyroid scintigraphy. He underwent total thyroidectomy, but pathological study did not reveal findings of thyroid carcinoma, but rather a hyperplastic nodule with hemorrhage. Strong cytoplasmic thyroglobulin immunostaining was observed, but sodium iodide symporter immunostaining was hardly detected in the hyperplastic nodule. The clinical characteristics of patients with thyroglobulin gene mutations are diverse, and some patients are diagnosed by chance on examination of goiter in adults. The presence of thyroid tumors that appear as cold nodules on thyroid scintigraphy should consider the potential for thyroid carcinoma, if the patient has relatively low serum thyroglobulin concentration in relation to the degree of TSH without thyroglobulin autoantibody.

  5. [Detection of lung nodules. New opportunities in chest radiography

    NARCIS (Netherlands)

    Pötter-Lang, S.; Schalekamp, S.; Schaefer-Prokop, C.M.; Uffmann, M.

    2014-01-01

    Chest radiography still represents the most commonly performed X-ray examination because it is readily available, requires low radiation doses and is relatively inexpensive. However, as previously published, many initially undetected lung nodules are retrospectively visible in chest radiographs.The

  6. Computer-aided diagnosis in chest radiography: beyond nodules.

    NARCIS (Netherlands)

    Ginneken, B. van; Hogeweg, L.E.; Prokop, M.

    2009-01-01

    Chest radiographs are the most common exam in radiology. They are essential for the management of various diseases associated with high mortality and morbidity and display a wide range of findings, many of them subtle. In this survey we identify a number of areas beyond pulmonary nodules that could

  7. Taxonomic studies of nodulated leguminous weeds from the flora of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-18

    May 18, 2009 ... Taxonomic studies of nodulated leguminous weeds from the flora of North Western part (Dera Ismail Khan) of Pakistan. Sarfaraz Khan Marwat*, Mir Ajab Khan, Mushtaq Ahmad, Muhammad Zafar, Farooq Ahmad and Abdul Nazir. Department of Plant Sciences, Quaid-i-Azam University Islamabad, Pakistan.

  8. Positron emission tomography of incidentally detected small pulmonary nodules

    DEFF Research Database (Denmark)

    Fischer, B M; Mortensen, J; Dirksen, A

    2004-01-01

    The aim of this study was to assess the value of fluorodeoxyglucose positron emission tomography (FDG PET) imaging of small pulmonary nodules incidentally detected by spiral computed tomography (CT) in a high-risk population. Ten patients (five females, five males, aged 54-72 years) were recruited...

  9. Differentiation of thyroid nodules using diffusion-weighted MRI ...

    African Journals Online (AJOL)

    Routine MRI of neck and diffusion-weighted MR imaging was performed using multiple b-values. Apparent diffusion coefficient (ADC) values were done for the different b-values. Histopathological results of the thyroidectomy samples were obtained. Comparison of apparent diffusion coefficient values of thyroid nodules with ...

  10. The frequency of carcinoma in solitary thyroid nodules and in ...

    African Journals Online (AJOL)

    Muhimbili Medical Centre, Dar es Salaam was made to determine the frequency of malignancy in patients with solitary non-toxic thyroid nodule (STN) and in those with multinodular goitre (MNG). There were 60 cases of STN and. 178 with MNG. Nodular goitre was found to be predominantly a disease of females with sex.

  11. Usefulness of ultrasonography is the evaluation of thyroid nodules.

    Science.gov (United States)

    Franco Uliaque, Carolina; Pardo Berdún, Francisco Javier; Laborda Herrero, Ricardo; Lórenz, Carmen Pérez

    2016-01-01

    To evaluate the diagnostic capacity of ultrasonography (US) for differentiating between malignant and benign thyroid nodules and its usefulness in obviating unnecessary invasive procedures. From January 2012 through December 2014, a total of 321 fine-needle aspiration biopsy (FNAB) procedures were done in 302 patients selected according to the criteria recommended by the American Association of Clinical Endocrinology guidelines and the American Thyroid Association guidelines. We analyzed the following characteristics on US: location, size, morphology, contour, consistency, echostructure, echogenicity, calcifications, and vascularization. We used univariate and multivariate analyses to investigate the relationship between the US findings and thyroid cancer. The prevalence of malignancy in our study population was 5.92%. The US findings that were significantly associated with a greater probability of malignancy were microcalcifications, central vascularization, and hypoechogenicity. The US findings that were associated with a lower risk of malignancy were areas of colloid degeneration and nodule heterogeneity. Our results suggest that decisions about whether to perform FNAB should be based on the presence of suspicious US findings found with our statistic model rather than on the size of the nodule. Thus, unnecessary FNAB procedures on nodules without suspicious US characteristics can be avoided. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

  12. Giant Ulcerative Lactating Nodule of Ectopic Breast Mimicking ...

    African Journals Online (AJOL)

    Objective: Lactating nodules occur in the pregnant and post partum patient and require investigation to rule out the possibility of a malignancy The aim of this paper is to ... Design and Setting: Case description, including clinical and pathological features, of a patient seen in Surgical Camp, Hoima, in September 2005.

  13. Mineralogical and geochemical studies of phosphorite nodules in ...

    African Journals Online (AJOL)

    Mineralogical and geochemical studies of phosphorite nodules in the Dange Formation Sokoto Basin, Northwestern Niveria. OA Adekeye, SO Akande. Abstract. No Abstract Available Journal of Mining and Geology Vol.40(2) 2004: 101-106. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT ...

  14. Nodulation and nitrogen fixation in common bean (Phaseolus vulgaris)

    African Journals Online (AJOL)

    Mamadou Gueye

    Nodulation and nitrogen fixation of field grown common bean (Phaseolus vulgaris) as influenced by fungicide seed treatment. Ndeye Fatou Diaw GUENE, Adama DIOUF and Mamadou GUEYE*. MIRCEN/ Laboratoire commun de microbiologie IRD-ISRA-UCAD, BP 1386, DAKAR, Senegal. Accepted 23 June 2003.

  15. Evaluation of subjectively assessed nodule traits of ostrich skins as ...

    African Journals Online (AJOL)

    Schalk Cloete

    according to standard procedures (Meyer et al., 2002). The skins were used to assess the acceptability of the nodules for market requirements, as determined through subjective scoring by 28 role-players in the ostrich leather production and marketing chain. These role-players consisted of primary producers (n = 7), skin.

  16. Effects of water stress on the rooting, nodulation potentials and ...

    African Journals Online (AJOL)

    Rooting, nodulation and growth ability of cowpea growing under limited water supply was investigated at the Teaching and Research Farm of the Imo State University, Owerri, Nigeria. The experiment was conducted in plastic buckets arranged in a completely Randomized Design with three replications, and treatments ...

  17. Profuse coarse pulmonary nodules in a patient with lymphangioleiomyomatosis

    DEFF Research Database (Denmark)

    Rasmussen, Daniel B; Shaker, Saher B; Seersholm, Niels

    2014-01-01

    Lymphangioleiomyomatosis (LAM) is a rare disease characterized by progressive cystic destruction of the lungs. We present an unusual radiological presentation of lymphangioleiomyomatosis in a patient followed for 33 years with profuse coarse lung nodules in addition to the classical cystic lesions...

  18. Nodulation and growth response of Sesbania sesban (L.) Merr. to ...

    African Journals Online (AJOL)

    A glasshouse experiment was carried out to study the effect of ammonium-N on the nodulation, growth and N-uptake of Sesbania sesban (L.) Merr. inoculated with an effective Mesorhizobium (S. sesban) strain. Ammonium-N was supplied twice weekly as 100 ml of nutrient solution at concentrations of 0, 100, 200, 400, 600 ...

  19. Nodulation, chlorophyll content and nitrogen yield of two woody ...

    African Journals Online (AJOL)

    Two field studies were conducted at the Teaching and Research Farm, Obafemi Awolowo University, Ile-Ife, Nigeria between 2000 and 2002 to compare the growth, nodulation, chlorophyll content and nitrogen accumulation of Leucaena leucocephala (Lam) de Wit cv. 28 and Gliricidia sepium (Jacq.) Walp cv. ILG50 at the ...

  20. Nodulation pattern and biodiversity of rhizobia of some important ...

    African Journals Online (AJOL)

    A collection of 20 root nodule bacteria were isolated from the hitherto unexplored indigenous woody legumes from Ethiopia. Their diversity was evaluated using numerical analyses on different morphological and physiological characteristics. Most of the isolates were found to be slow-growing, sensitive to high concentration ...

  1. Nitrogen fixation and nodulation of soybean as affected by rhizobial ...

    African Journals Online (AJOL)

    The study evaluated the efficacy of different adhesives added to rhizobial seed inoculum on soybean nodulation and biological nitrogen fixation in a screen house and under field conditions. The experiment was a 6×3 factorial arranged in Completely Randomized Design and Randomized Complete Block Design for the pot ...

  2. Taxonomic studies of nodulated leguminous weeds from the flora of ...

    African Journals Online (AJOL)

    Taxonomic studies of nodulated leguminous weeds from the flora of North Western part (Dera Ismail Khan) of Pakistan. ... Results were systematically arranged by alphabetic order of botanical names, followed by synonyms (if any), description of the plant, flowering and fruiting period, type, local and general distribution.

  3. Micromonospora is a normal occupant of actinorhizal nodules

    Indian Academy of Sciences (India)

    These nodules all have a peripheral cortex with enlarged cells filled with Frankia hyphae and vesicles. Isolation in pure culture has been notoriously difficult, due in a large part to the growth of fast-growing contaminants where, it was later found, Frankia was slow-growing. Many of these contaminants, which were later found ...

  4. The Rationale for Treating the Nodule in Dupuytren's Disease.

    Science.gov (United States)

    Ketchum, Lynn D

    2014-12-01

    Dupuytren's disease encompasses a spectrum of fibroblastic disorders from the presence of 1-2 nodules in the palm of a hand with no joint contracture to grotesque, crippling and disabling deformities of hands. Over the last 50 years, many enlightening studies have been forthcoming, which, through techniques of histopathology, biochemistry, tissue culture, and electron microscopy, have shed pearls of light on various aspects of the disease process. A comprehensive review of the literature on Dupuytren's disease was undertaken, stringing together results from numerous studies to establish a table of events and their location in the development of the disease. What will be seen is a credible scenario of events which will enable the clinician to be more proactive in the earlier treatment of the disease and more aware of factors that increase or decrease recurrence rates postoperatively. The most effective management of Dupuytren's disease is early recognition and treatment of the nodule, before the development of a joint contracture, particularly of a proximal interphalangeal joint. As there is evidence of a significant inflammatory role in the development of the nodule, the process of fibroplasia can be minimized by altering the macrophage > fibroblast > collagen cascade by the intralesional injection of a potent anti-inflammatory agent such as triamcinolone, which also blocks tissue inhibitors of collagenase, thus enhancing the action of native collagenase, and reduces the size and firmness of nodules and, at least temporarily, arrests their progression.

  5. Root-nodule bacteria isolated from native Amphithalea ericifolia and ...

    African Journals Online (AJOL)

    Indigenous root-nodule bacteria isolated from the acid sands of the Cape using Aspalathus linearis, Aspalathus hispida, Aspalathus carnosa, Aspalathus capensis and Amphithalea ericifolia as trap hosts showed considerable tolerance to low pH. Isolates from A. ericifolia and A. carnosa could even grow in YMB medium at ...

  6. Formation of multiple pulmonary nodules during treatment with leflunomide

    Directory of Open Access Journals (Sweden)

    Gilberto Toshikawa Yoshikawa

    2015-06-01

    Full Text Available Pulmonary involvement is one of the extra-articular manifestations of rheumatoid arthritis and can be due to the disease itself or secondary to the medications used in order to treat it. We report the case of a 60-year-old woman who had been diagnosed with rheumatoid arthritis and developed multiple pulmonary nodules during treatment with leflunomide.

  7. A new design concept for nodule mining system

    Digital Repository Service at National Institute of Oceanography (India)

    Janakiraman, G.; Venkatesan, R.; Rajaraman, V.S.

    An overview is presented on the hazards associated with various types of equipment to be used for the commercial mining of nodules from the seabed. The design of a suitable mining collector and the various options available are discussed. A novel...

  8. {sup 10}Be in rhodochrosite nodules from Neogene sediments along the Galapagos Ridge, equatorial Pacific

    Energy Technology Data Exchange (ETDEWEB)

    Aldahan, A., E-mail: ala.aldahan@geo.uu.s [Department of Earth Sciences, Uppsala University, Uppsala (Sweden); Department of Geology, United Arab Emirates University, Al Ain (United Arab Emirates); Morad, S. [Department of Earth Sciences, Uppsala University, Uppsala (Sweden); Department of Petroleum Geosciences, Petroleum Institute, Abu Dhabi (United Arab Emirates); Possnert, G. [Tandem Laboratory, Uppsala University, Uppsala (Sweden); Sturesson, U. [Department of Earth Sciences, Uppsala University, Uppsala (Sweden); ElSaiy, A. [Department of Geology, United Arab Emirates University, Al Ain (United Arab Emirates)

    2010-04-15

    Microcrystalline, calcian rhodochrosite occurs as nodules around burrows in late Neogene pelagic sediments from the Galapagos Ridge in the Guatemala Basin, eastern equatorial Pacific (DSDP Leg 68; Site 503). {sup 10}Be isotope revealed that the rhodochrosite nodules have formed under growth conditions much faster than those reported for Fe-Mn nodules. The overall REE patterns of the nodules and host pelagic sediments indicate element derivation mainly from marine pore water. However, variations in the shale normalised Eu values suggest influx of hydrothermal fluids into mounds area at Galapagos, which is also evidenced by the similar minor and major element contents in the nodules and host sediments.

  9. Redox regulation of peroxiredoxin and proteinases by ascorbate and thiols during pea root nodule senescence.

    Science.gov (United States)

    Groten, Karin; Dutilleul, Christelle; van Heerden, Philippus D R; Vanacker, Hélène; Bernard, Stéphanie; Finkemeier, Iris; Dietz, Karl-Josef; Foyer, Christine H

    2006-02-20

    Redox factors contributing to nodule senescence were studied in pea. The abundance of the nodule cytosolic peroxiredoxin but not the mitochondrial peroxiredoxin protein was modulated by ascorbate. In contrast to redox-active antioxidants such as ascorbate and cytosolic peroxiredoxin that decreased during nodule development, maximal extractable nodule proteinase activity increased progressively as the nodules aged. Cathepsin-like activities were constant throughout development but serine and cysteine proteinase activities increased during senescence. Senescence-induced cysteine proteinase activity was inhibited by cysteine, dithiotreitol, or E-64. Senescence-dependent decreases in redox-active factors, particularly ascorbate and peroxiredoxin favour decreased redox-mediated inactivation of cysteine proteinases.

  10. Morphogenesis of root nodules in white clover. II. The effect of mutation in genes nod IJ of the microsymbiont upon the nodule structure

    Directory of Open Access Journals (Sweden)

    Barbara Łotocka

    2014-01-01

    Full Text Available Morphogenesis of ineffective root nodules initiated on the roots of white clover 'Astra' by the Rhizobium leguminosarum biovar. trifolii strains ANU261 (Tn5 insertion in nod 1 gene and ANU262 (Tn5 insertion in nod J gene was investigated. Following changes were observed, as compared to the wild-type nodulation: the exaggerated, not delayed reaction of root hairs; the delay in nodulation with the number of nodules the same as in plants inoculated with a wild strain; the formation and organization of the nodule primordium not changed in comparison with the wild-type nodules; infection threads abnormally branched and diffusing with bacteria deprived of light zone and enriched with storage material; infected cells of bacteroidal tissue abnormally strongly osmiophilic and only slightly vacuolated; symbiosomes with very narrowed peribacteroidal space, subject to premature degradation; abnormal accumulation of starch in the nodule tissues; nodule development blocked at the stage of laterally situated meristem and single nodule bundle; inhibition of divisions in the meristem and vacuolation of its cells; the appearance of single cells with colonies of saprophytic rhizobia embedded in the fibrillar matrix in the old, degraded regions of the bacteroidal tissue.

  11. Improved efficiency of CT interpretation using an automated lung nodule matching program.

    Science.gov (United States)

    Koo, Chi Wan; Anand, Vikram; Girvin, Francis; Wickstrom, Maj L; Fantauzzi, John P; Bogoni, Luca; Babb, James S; Ko, Jane P

    2012-07-01

    The purpose of this study was to assess the impact of an automated program on improvement in lung nodule matching efficiency. Four thoracic radiologists independently reviewed two serial chest CT examinations from each of 57 patients. Each radiologist performed timed manual lung nodule matching. After 6 weeks, all radiologists independently repeated the timed matching portion using an automated nodule matching program. The time required for manual and automated matching was compared. The impact of nodule size and number on matching efficiency was determined. An average of 325 (range, 244-413) noncalcified solid pulmonary nodules was identified. Nodule matching was significantly faster with the automated program irrespective of the interpreting radiologist (p 0.5). The automated program achieved 90%, 90%, 79%, and 92% accuracy for the four readers. The improvement in efficiency for a given patient using the automated technique was proportional to the number of matched nodules (p < 0.0001) and inversely proportional to nodule size (p < 0.05). Use of the automated lung nodule matching program significantly improves diagnostic efficiency. The time saved is proportionate to the number of nodules identified and inversely proportional to nodule size. Adoption of such a program should expedite CT examination interpretation and improve report turnaround time.

  12. Towards automatic pulmonary nodule management in lung cancer screening with deep learning

    Science.gov (United States)

    Ciompi, Francesco; Chung, Kaman; van Riel, Sarah J.; Setio, Arnaud Arindra Adiyoso; Gerke, Paul K.; Jacobs, Colin; Th. Scholten, Ernst; Schaefer-Prokop, Cornelia; Wille, Mathilde M. W.; Marchianò, Alfonso; Pastorino, Ugo; Prokop, Mathias; van Ginneken, Bram

    2017-04-01

    The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers.

  13. Towards automatic pulmonary nodule management in lung cancer screening with deep learning.

    Science.gov (United States)

    Ciompi, Francesco; Chung, Kaman; van Riel, Sarah J; Setio, Arnaud Arindra Adiyoso; Gerke, Paul K; Jacobs, Colin; Scholten, Ernst Th; Schaefer-Prokop, Cornelia; Wille, Mathilde M W; Marchianò, Alfonso; Pastorino, Ugo; Prokop, Mathias; van Ginneken, Bram

    2017-04-19

    The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers.

  14. Correlation between the Quantifiable Parameters of Whole Solitary Pulmonary Nodules Perfusion Imaging Derived with Dynamic CT and Nodules Size

    Directory of Open Access Journals (Sweden)

    Shiyuan LIU

    2009-05-01

    Full Text Available Background and objective The solitary pulmonary nodules (SPNs is one of the most common findings on chest radiographs. The blood flow patterns of the biggest single SPNs level has been studied. This assessment may be only a limited sample of the entire region of interest (ROI and is unrepresentative of the SPNs as a volume. Ideally, SPNs volume perfusion should be measured. The aim of this study is to evaluate the correlation between the quantifiableparameters of SPNs volume perfusion imaging derived with 16-slice spiral CT and 64-slice spiral CT and nodules size. Methods Sixty-five patients with SPNs (diameter≤3 cm; 42 malignant; 12 active inflammatory; 11 benign underwent multi-location dynamic contrast material-enhanced serial CT scanning mode with stable table were performed; The mean values of valid sections were calculated, as the quantifiable parameters of volume SPNs perfusion imaging derived with16-slice spiral CT and 64-slice spiral CT. The correlation between the quantifiable parameters of SPNs volume perfusion imaging derived with 16-slice spiral CT and 64-slice spiral CT and nodules size were assessed by means of linear regression analysis. Results No significant correlations were found between the nodules size and each of the peak height (PHSPN (32.15 Hu±14.55 Hu,ratio of peak height of the SPN to that of the aorta (SPN-to-A ratio(13.20±6.18%, perfusion(PSPN (29.79±19.12 mLmin-1100 g-1 and mean transit time (12.95±6.53 s (r =0.081, P =0.419; r =0.089, P =0.487; r =0.167, P =0.077; r =0.023, P =0.880. Conclusion No significant correlations were found between the quantifiable parameters of SPNs volume perfusion imaging derived with 16-slice spiral CT and 64-slice spiral CT and nodules size.

  15. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

    Science.gov (United States)

    Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

    2016-01-01

    Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance. PMID:27864511

  16. Classification of pulmonary nodules in lung CT images using shape and texture features

    Science.gov (United States)

    Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Dutta, Anirvan; Garg, Mandeep; Khandelwal, Niranjan; Kumar, Prafulla

    2016-03-01

    Differentiation of malignant and benign pulmonary nodules is important for prognosis of lung cancer. In this paper, benign and malignant nodules are classified using support vector machine. Several shape-based and texture-based features are used to represent the pulmonary nodules in the feature space. A semi-automated technique is used for nodule segmentation. Relevant features are selected for efficient representation of nodules in the feature space. The proposed scheme and the competing technique are evaluated on a data set of 542 nodules of Lung Image Database Consortium and Image Database Resource Initiative. The nodules with composite rank of malignancy "1","2" are considered as benign and "4","5" are considered as malignant. Area under the receiver operating characteristics curve is 0:9465 for the proposed method. The proposed method outperforms the competing technique.

  17. A qualitative study of the nodulating ability of legumes of Pakistan

    Directory of Open Access Journals (Sweden)

    Mohammad Athar

    2014-01-01

    Full Text Available Legume-Rhizobium symbiosis accumulates substantial amounts of mineralizable nitrogen which help in ecological rehabilitation of degraded soils and increase the soil fertility in agricultural ecosystem. Nodulation was studied in 72 legume species from various parts of Pakistan. All the species of Papilionoideae and Mimosoideae were nodulated whereas all the species examined in Caesalpinioideae were non-nodulated. Attempts to elicit nodulation in Caesalpinioid species by rhizobial inoculation were not successful and they were accepted as lacking nodulating ability. Nodulation is reported for the first time in 6 species within 3 genera of Mimosoideae and 9 species within 5 genera of Papilionoideae. Majority of the species were abundantly nodulated under natural soil conditions or when grown in uninoculated garden soil indicating distribution of wide range of naturalized rhizobia. The study shows that the wild legumes hold great promise for inclusion in revegetation of denuded and derelict ecosystems.

  18. Advances in intelligent diagnosis methods for pulmonary ground-glass opacity nodules.

    Science.gov (United States)

    Yang, Jing; Wang, Hailin; Geng, Chen; Dai, Yakang; Ji, Jiansong

    2018-02-07

    Pulmonary nodule is one of the important lesions of lung cancer, mainly divided into two categories of solid nodules and ground glass nodules. The improvement of diagnosis of lung cancer has significant clinical significance, which could be realized by machine learning techniques. At present, there have been a lot of researches focusing on solid nodules. But the research on ground glass nodules started late, and lacked research results. This paper summarizes the research progress of the method of intelligent diagnosis for pulmonary nodules since 2014. It is described in details from four aspects: nodular signs, data analysis methods, prediction models and system evaluation. This paper aims to provide the research material for researchers of the clinical diagnosis and intelligent analysis of lung cancer, and further improve the precision of pulmonary ground glass nodule diagnosis.

  19. The effects of computed tomography with iterative reconstruction on solid pulmonary nodule volume quantification.

    Directory of Open Access Journals (Sweden)

    Martin J Willemink

    Full Text Available BACKGROUND: The objectives of this study were to evaluate the influence of iterative reconstruction (IR on pulmonary nodule volumetry with chest computed tomography (CT. METHODS: Twenty patients (12 women and 8 men, mean age 61.9, range 32-87 underwent evaluation of pulmonary nodules with a 64-slice CT-scanner. Data were reconstructed using filtered back projection (FBP and IR (Philips Healthcare, iDose(4-levels 2, 4 and 6 at similar radiation dose. Volumetric nodule measurements were performed with semi-automatic software on thin slice reconstructions. Only solid pulmonary nodules were measured, no additional selection criteria were used for the nature of nodules. For intra-observer and inter-observer variability, measurements were performed once by one observer and twice by another observer. Algorithms were compared using the concordance correlation-coefficient (pc and Friedman-test, and post-hoc analysis with the Wilcoxon-signed ranks-test with Bonferroni-correction (significance-level p<0.017. RESULTS: Seventy-eight nodules were present including 56 small nodules (volume<200 mm(3, diameter<8 mm and 22 large nodules (volume≥200 mm(3, diameter≥8 mm. No significant differences in measured pulmonary nodule volumes between FBP, iDose(4-levels 2, 4 and 6 were found in both small nodules and large nodules. FBP and iDose(4-levels 2, 4 and 6 were correlated with pc-values of 0.98 or higher for both small and large nodules. Pc-values of intra-observer and inter-observer variability were 0.98 or higher. CONCLUSIONS: Measurements of solid pulmonary nodule volume measured with standard-FBP were comparable with IR, regardless of the IR-level and no significant differences between measured volumes of both small and large solid nodules were found.

  20. Sonographically guided fine-needle biopsy of thyroid nodules: the effects of nodule characteristics, sampling technique, and needle size on the adequacy of cytological material

    International Nuclear Information System (INIS)

    Degirmenci, B.; Haktanir, A.; Albayrak, R.; Acar, M.; Sahin, D.A.; Sahin, O.; Yucel, A.; Caliskan, G.

    2007-01-01

    Aim: To evaluate the effects of sonographic characteristics of thyroid nodules, the diameter of needle used for sampling, and sampling technique on obtaining sufficient cytological material (SCM). Materials and methods: We performed sonography-guided fine-needle biopsy (FNB) in 232 solid thyroid nodules. Size-, echogenicity, vascularity, and localization of all nodules were evaluated by Doppler sonography before the biopsy. Needles of size 20, 22, and 24 G were used for biopsy. The biopsy specimen was acquired using two different methods after localisation. In first method, the needle tip was advanced into the nodule in various positions using a to-and-fro motion whilst in the nodule, along with concurrent aspiration. In the second method, the needle was advanced vigorously using a to-and-fro motion within the nodule whilst being rotated on its axis (capillary-action technique). Results: The mean nodule size was 2.1 ± 1.3 cm (range 0.4-7.2 cm). SCM was acquired from 154 (66.4%) nodules by sonography-guided FNB. In 78 (33.6%) nodules, SCM could not be collected. There was no significant difference between nodules with different echogenicity and vascularity for SCM. Regarding the needle size, the lowest rate of SCM was obtained using 20 G needles (56.6%) and the highest rate of adequate material was obtained using 24 G needles (82.5%; p = 0.001). The SCM rate was 76.9% with the capillary-action technique versus 49.4% with the aspiration technique (p < 0.001). Conclusion: Selecting finer needles (24-25 G) for sonography-guided FNB of thyroid nodules and using the capillary-action technique decreased the rate of inadequate material in cytological examination

  1. System and method for producing metallic iron nodules

    Science.gov (United States)

    Bleifuss, Rodney L [Grand Rapids, MN; Englund, David J [Bovey, MN; Iwasaki, Iwao [Grand Rapids, MN; Lindgren, Andrew J [Grand Rapids, MN; Kiesel, Richard F [Hibbing, MN

    2011-09-20

    A method for producing metallic iron nodules by assembling a shielding entry system to introduce coarse carbonaceous material greater than 6 mesh in to the furnace atmosphere at location(s) where the temperature of the furnace atmosphere adjacent at least partially reduced reducible iron bearing material is between about 2200 and 2650.degree. F. (1200 and 1450.degree. C.), the shielding entry system adapted to inhibit emission of infrared radiation from the furnace atmosphere and seal the furnace atmosphere from exterior atmosphere while introducing coarse carbonaceous material greater than 6 mesh into the furnace to be distributed over the at least partially reduced reducible iron bearing material, and heating the covered at least partially reduced reducible iron bearing material in a fusion atmosphere to assist in fusion and inhibit reoxidation of the reduced material during fusion to assist in fusion and inhibit reoxidation of the reduced material in forming metallic iron nodules.

  2. Marine biominerals: perspectives and challenges for polymetallic nodules and crusts.

    Science.gov (United States)

    Wang, Xiaohong; Müller, Werner E G

    2009-06-01

    Deep sea minerals in polymetallic nodules, crusts and hydrothermal vents are not only formed by mineralization but also by biologically driven processes involving microorganisms (biomineralization). Within the nodules, free-living and biofilm-forming bacteria provide the matrix for manganese deposition, and in cobalt-rich crusts, coccolithophores represent the dominant organisms that act as bio-seeds for an initial manganese deposition. These (bio)minerals are economically important: manganese is an important alloying component and cobalt forms part of special steels in addition to being used, along with other rare metals, in plasma screens, hard-disk magnets and hybrid car motors. Recent progress in our understanding of the participation of the organic matrices in the enrichment of these metals might provide the basis for feasibility studies of biotechnological applications.

  3. Evaluation of radiographic imaging techniques in lung nodule detection

    International Nuclear Information System (INIS)

    Ho, J.T.; Kruger, R.A.

    1989-01-01

    Dual-energy radiography appears to be the most effective technique to address bone superposition that compromises conventional chest radiography. A dual-energy, single-exposure, film-based technique was compared with a dual-energy, dual-exposure technique and conventional chest radiography in a simulated lung nodule detection study. Observers detected more nodules on images produced by dual-energy techniques than on images produced by conventional chest radiography. The difference between dual-energy and conventional chest radiography is statistically significant and the difference between dual-energy, dual-exposure and single-exposure techniques is statistically insignificant. The single-exposure technique has the potential to replace the dual-exposure technique in future clinical application

  4. Inference method using bayesian network for diagnosis of pulmonary nodules

    International Nuclear Information System (INIS)

    Kawagishi, Masami; Iizuka, Yoshio; Yamamoto, Hiroyuki; Yakami, Masahiro; Kubo, Takeshi; Fujimoto, Koji; Togashi, Kaori

    2010-01-01

    This report describes the improvements of a naive Bayes model that infers the diagnosis of pulmonary nodules in chest CT images based on the findings obtained when a radiologist interprets the CT images. We have previously introduced an inference model using a naive Bayes classifier and have reported its clinical value based on evaluation using clinical data. In the present report, we introduce the following improvements to the original inference model: the selection of findings based on correlations and the generation of a model using only these findings, and the introduction of classifiers that integrate several simple classifiers each of which is specialized for specific diagnosis. These improvements were found to increase the inference accuracy by 10.4% (p<.01) as compared to the original model in 100 cases (222 nodules) based on leave-one-out evaluation. (author)

  5. Computer-aided diagnosis (CAD) of subsolid nodules: Evaluation of a commercial CAD system

    International Nuclear Information System (INIS)

    Benzakoun, Joseph; Bommart, Sébastien; Coste, Joël; Chassagnon, Guillaume; Lederlin, Mathieu; Boussouar, Samia

    2016-01-01

    Highlights: • CAD sensitivity is still limited for automated detection of subsolid nodules. • CAD detection rate is higher for part-solid than for pure ground-glass nodules. • Part-solid nodule detection is not better for nodules with larger solid component. - Abstract: Objectives: To evaluate the performance of a commercially available CAD system for automated detection and measurement of subsolid nodules. Materials and methods: The CAD system was tested on 50 pure ground-glass and 50 part-solid nodules (median diameter: 17 mm) previously found on standard-dose CT scans in 100 different patients. True nodule detection and the total number of CAD marks were evaluated at different sensitivity settings. The influence of nodule and CT acquisition characteristics was analyzed with logistic regression. Software and manually measured diameters were compared with Spearman and Bland-Altman methods. Results: With sensitivity adjusted for 3-mm nodule detection, 50/100 (50%) subsolid nodules were detected, at the average cost of 17 CAD marks per CT. These figures were respectively 26/100 (26%) and 2 at the 5-mm setting. At the highest sensitivity setting (2-mm nodule detection), the average number of CAD marks per CT was 41 but the nodule detection rate only increased to 54%. Part–solid nodules were better detected than pure ground glass nodules: 36/50 (72%) versus 14/50 (28%) at the 3-mm setting (p < 0.0001), with no influence of the solid component size. Except for the type (i.e. part solid or pure ground glass), no other nodule characteristic influenced the detection rate. High-quality segmentation was obtained for 79 nodules, which for automated measurements correlated well with manual measurements (rho = 0.90[0.84–0.93]). All part-solid nodules had software-measured attenuation values above −671 Hounsfield units (HU). Conclusion: The detection rate of subsolid nodules by this CAD system was insufficient, but high-quality segmentation was obtained in 79% of

  6. Computer-aided diagnosis (CAD) of subsolid nodules: Evaluation of a commercial CAD system

    Energy Technology Data Exchange (ETDEWEB)

    Benzakoun, Joseph, E-mail: benzakoun.joseph@gmail.com [Hôpital Hôtel-Dieu, 1 parvis Notre-Dame, 75004 Paris (France); Université Paris Descartes, 12 rue de l’Ecole de Médecine, 75006 Paris (France); Bommart, Sébastien, E-mail: s-bommart@chu-montpellier.fr [CHU de Montpellier, 191 avenue du Doyen Gaston Giraud, 34000 Montpellier (France); INSERM U 1046, 371 avenue du Doyen G. Giraud, 34000 Montpellier (France); Coste, Joël, E-mail: joel.coste@htd.aphp.fr [Hôpital Hôtel-Dieu, 1 parvis Notre-Dame, 75004 Paris (France); Université Paris Descartes, 12 rue de l’Ecole de Médecine, 75006 Paris (France); Chassagnon, Guillaume, E-mail: gchassagnon@gmail.com [Université Paris Descartes, 12 rue de l’Ecole de Médecine, 75006 Paris (France); Hôpital Cochin, Radiologie, 27 rue du Faubourg Saint Jacques, 75014 Paris (France); Lederlin, Mathieu, E-mail: mathieu.lederlin@chu-rennes.fr [CHU de Rennes, Radiologie, 2 Rue Henri le Guilloux, 35000 Rennes (France); Université de Rennes 1, 9 Rue Jean Macé, 35000 Rennes (France); Boussouar, Samia, E-mail: samiaboussouar@gmail.com [Université Paris Descartes, 12 rue de l’Ecole de Médecine, 75006 Paris (France); Hôpital Européen Georges Pompidou, 20 Rue Leblanc, 75015 Paris (France); and others

    2016-10-15

    Highlights: • CAD sensitivity is still limited for automated detection of subsolid nodules. • CAD detection rate is higher for part-solid than for pure ground-glass nodules. • Part-solid nodule detection is not better for nodules with larger solid component. - Abstract: Objectives: To evaluate the performance of a commercially available CAD system for automated detection and measurement of subsolid nodules. Materials and methods: The CAD system was tested on 50 pure ground-glass and 50 part-solid nodules (median diameter: 17 mm) previously found on standard-dose CT scans in 100 different patients. True nodule detection and the total number of CAD marks were evaluated at different sensitivity settings. The influence of nodule and CT acquisition characteristics was analyzed with logistic regression. Software and manually measured diameters were compared with Spearman and Bland-Altman methods. Results: With sensitivity adjusted for 3-mm nodule detection, 50/100 (50%) subsolid nodules were detected, at the average cost of 17 CAD marks per CT. These figures were respectively 26/100 (26%) and 2 at the 5-mm setting. At the highest sensitivity setting (2-mm nodule detection), the average number of CAD marks per CT was 41 but the nodule detection rate only increased to 54%. Part–solid nodules were better detected than pure ground glass nodules: 36/50 (72%) versus 14/50 (28%) at the 3-mm setting (p < 0.0001), with no influence of the solid component size. Except for the type (i.e. part solid or pure ground glass), no other nodule characteristic influenced the detection rate. High-quality segmentation was obtained for 79 nodules, which for automated measurements correlated well with manual measurements (rho = 0.90[0.84–0.93]). All part-solid nodules had software-measured attenuation values above −671 Hounsfield units (HU). Conclusion: The detection rate of subsolid nodules by this CAD system was insufficient, but high-quality segmentation was obtained in 79% of

  7. Computer-aided detection of lung nodules on multidetector row computed tomography using three-dimensional analysis of nodule candidates and their surroundings

    International Nuclear Information System (INIS)

    Matsumoto, Sumiaki; Ohno, Yoshiharu; Takenaka, Daisuke; Sugimura, Kazuro; Yamagata, Hitoshi

    2008-01-01

    We have been developing a computer-aided detection (CAD) system for lung nodules on multidetector row computed tomography (MDCT). The scheme for nodule detection in this system is featured by three-dimensional analysis for nodule detection in nodules and their surroundings, which is designed to discriminate nodules from blood vessels. The purpose of this study was to evaluate the CAD system. MDCT images from 30 patients with lung nodules were read twice, 3 weeks apart by a chest radiologist to detect noncalcified nodules of ≥4 mm. The first reading was without CAD, and the second reading was with CAD. Based on the reference standard later determined by another chest radiologist, the sensitivity of the former chest radiologist without or with CAD was obtained; the sensitivity and false-positive rate of the system alone were also obtained. The reference standard consisted of 66 nodules. The sensitivity of the chest radiologist was 77% (51/66) without CAD and 91% (60/66) with CAD, showing a significant improvement. The CAD system alone showed a sensitivity of 79% (52/66) with the false-positive rate of 4.5 per patient. Although preliminary, these results indicate the efficacy of the CAD system. (author)

  8. Radiofrequency thermal ablation of a metastatic lung nodule

    Energy Technology Data Exchange (ETDEWEB)

    Highland, Adrian M. [Department of Clinical Radiology, Hull Royal Infirmary, Anlaby Road, Hull, HU3 2JZ (United Kingdom); Mack, Paul [Diana Princess of Wales Hospital, Scartho Road, Grimsby, DN33 2BA (United Kingdom); Breen, David J. [Department of Radiology, Southampton University Hospitals, Tremona Road, Southampton, SO16 6YD (United Kingdom)

    2002-07-01

    Pulmonary metastases are a common finding in patients with colonic adenocarcinoma. We report the treatment of a metastatic lung nodule with radiofrequency (RF) ablation under CT guidance. This case illustrates the use of RF ablation in a patient in whom surgical resection was no longer possible and where chemotherapy was unlikely to produce benefit. This technique may offer a viable method of cytoreduction when other treatments have not succeeded. (orig.)

  9. Radiofrequency thermal ablation of a metastatic lung nodule

    International Nuclear Information System (INIS)

    Highland, Adrian M.; Mack, Paul; Breen, David J.

    2002-01-01

    Pulmonary metastases are a common finding in patients with colonic adenocarcinoma. We report the treatment of a metastatic lung nodule with radiofrequency (RF) ablation under CT guidance. This case illustrates the use of RF ablation in a patient in whom surgical resection was no longer possible and where chemotherapy was unlikely to produce benefit. This technique may offer a viable method of cytoreduction when other treatments have not succeeded. (orig.)

  10. 2009 American Thyroid Association guidelines on thyroid nodules.

    Science.gov (United States)

    Perros, P

    2010-08-01

    The American Thyroid Association guidelines on thyroid nodules and differentiated thyroid cancer, published in 2009, provide valuable recommendations based on current evidence. Inevitably, controversies and uncertainties will continue to challenge clinicians and patients. On topics where evidence is not clear-cut, judgement may be coloured by pre-existing practises and the structure of the health service in each country, so one has to be aware of the pitfalls of transferring recommendations to one's own practise.

  11. Vocal nodules in a colombian teachers group with dysphonia

    OpenAIRE

    Andrés Felipe Alvarado Díaz; Carlos Eduardo Pinzón; José Rafael Tovar Cuevas; Adriana Fajardo Hoyos

    2013-01-01

    Objectives: This study determined the prevalence of vocal nodules associated with dysphonia in teachers aged from 35 to 65 years, taking into consideration both individual and occupational variables. Methodology: Descriptive study that included the information contained in 262 medical records of teachers diagnosed with dysphonia in occupational health consultations at the institutions that provide health services in Bogotá, Colombia from March 2009 to March 2012. The presence of laryngeal nod...

  12. Thyroid nodule guidelines: agreement, disagreement and need for future research

    DEFF Research Database (Denmark)

    Paschke, Ralf; Hegedüs, Laszlo; Alexander, Erik

    2011-01-01

    This article reviews agreement, disagreement and need for future research of the thyroid nodule guidelines published by the British Thyroid Association, National Cancer Institute, American Thyroid Association and the joint, transatlantic effort of three large societies, the American Society...... of Clinical Endocrinologists, Associazione Medici Endocrinologi and the European Thyroid Association, published in 2010. Consensus exists for most topics in the various guidelines. A few areas of disagreement, such as the use of scintigraphy, are mostly due to differences in disease prevalence in different...

  13. How to Differentiate Borderline Hepatic Nodules in Hepatocarcinogenesis: Emphasis on Imaging Diagnosis.

    Science.gov (United States)

    Park, Hyun Jeong; Choi, Byung Ihn; Lee, Eun Sun; Park, Sung Bin; Lee, Jong Beum

    2017-06-01

    Rapid advances in liver imaging have improved the evaluation of hepatocarcinogenesis and early diagnosis and treatment of hepatocellular carcinoma (HCC). In this situation, detection of early-stage HCC in its development is important for the improvement of patient survival and optimal treatment strategies. Because early HCCs are considered precursors of progressed HCC, precise differentiation between a dysplastic nodule (DN), especially a high-grade DN, and early HCC is important. In clinical practice, these nodules are frequently called "borderline hepatic nodules." This article discusses radiological and pathological characteristics of these borderline hepatic nodules and offers an understanding of multistep hepatocarcinogenesis by focusing on the descriptions of the imaging changes in the progression of DN and early HCC. Detection and accurate diagnosis of borderline hepatic nodules are still a challenge with contrast enhanced ultrasonography, CT, and MRI with extracellular contrast agents. However, gadoxetic acid-enhanced MRI may be useful for improving the diagnosis of these borderline nodules. Since there is a net effect of incomplete neoangiogenesis and decreased portal venous flow in the early stage of hepatocarcinogenesis, borderline hepatic nodules commonly show iso- or hypovascularity. Therefore, precise differentiation of these nodules remains a challenging issue. In MRI using hepatobiliary contrast agents, signal intensity of HCCs on hepatobiliary phase (HBP) is regarded as a potential imaging biomarker. Borderline hepatic nodules are seen as nonhypervascular and hypointense nodules on the HBP, which is important for predicting tumor behavior and determining appropriate therapeutic strategies.

  14. Significance of pulmonary nodules in multi-detector computed tomography scan of noncancerous patients

    Directory of Open Access Journals (Sweden)

    Ali Toghiani

    2015-01-01

    Full Text Available Background: Computed tomography (CT scan is one the most useful devices in chest imaging. CT scan can be used in mediastinal abnormality, lungs, and pleural evaluations. According to the high prevalence and different causes of pulmonary nodules, we designed this study to evaluate the prevalence and the types of pulmonary nodules in noncancerous patients who underwent chest multi-detector CT (MDCT scan. Materials and Methods: This was a cross-sectional study which was in our hospital to evaluate the prevalence of pulmonary nodules in noncancerous patients who underwent MDCT. A checklist was used for data collection containing number, location, size, and shape of pulmonary nodules if present in CT scan, and we also included patient′s age and history of smoking. We analyzed the data with Statistical Program for Social Sciences software (version 18. Results: In this study, 115 patients (40% had a pulmonary nodule. The mean number of a total nodule in each patient was 0.8 ± 0.07. Mean number of intra-parenchymal, sub pleural, and perivascular nodules were 0.34 ± 0.04, 0.31 ± 0.04, and 0.14 ± 0.02, respectively. The mean number of calcified nodules was 0.13 ± 0.02. There was no significant correlation between age and nodule characteristics (P > 0.05. Conclusion: The prevalence of pulmonary nodules was quite frequent in MDCT scan of noncancerous cases. So, it should not be overvalued in noncancerous cases.

  15. Significance of pulmonary nodules in multi-detector computed tomography scan of noncancerous patients

    Science.gov (United States)

    Toghiani, Ali; Adibi, Atoosa; Taghavi, Arash

    2015-01-01

    Background: Computed tomography (CT) scan is one the most useful devices in chest imaging. CT scan can be used in mediastinal abnormality, lungs, and pleural evaluations. According to the high prevalence and different causes of pulmonary nodules, we designed this study to evaluate the prevalence and the types of pulmonary nodules in noncancerous patients who underwent chest multi-detector CT (MDCT) scan. Materials and Methods: This was a cross-sectional study which was in our hospital to evaluate the prevalence of pulmonary nodules in noncancerous patients who underwent MDCT. A checklist was used for data collection containing number, location, size, and shape of pulmonary nodules if present in CT scan, and we also included patient's age and history of smoking. We analyzed the data with Statistical Program for Social Sciences software (version 18). Results: In this study, 115 patients (40%) had a pulmonary nodule. The mean number of a total nodule in each patient was 0.8 ± 0.07. Mean number of intra-parenchymal, sub pleural, and perivascular nodules were 0.34 ± 0.04, 0.31 ± 0.04, and 0.14 ± 0.02, respectively. The mean number of calcified nodules was 0.13 ± 0.02. There was no significant correlation between age and nodule characteristics (P > 0.05). Conclusion: The prevalence of pulmonary nodules was quite frequent in MDCT scan of noncancerous cases. So, it should not be overvalued in noncancerous cases. PMID:26487874

  16. Biologic origin of iron nodules in a marine terrace chronosequence, Santa Cruz, California

    Science.gov (United States)

    Schulz, M.S.; Vivit, D.; Schulz, C.; Fitzpatrick, J.; White, A.

    2010-01-01

    The distribution, chemistry, and morphology of Fe nodules were studied in a marine terrace soil chronosequence northwest of Santa Cruz, California. The Fe nodules are found at depths <1 m on all terraces. The nodules consisted of soil mineral grains cemented by Fe oxides. The nodules varied in size from 0.5 to 25 mm in diameter. Nodules did not occur in the underlying regolith. The Fe-oxide mineralogy of the nodules was typically goethite; however, a subset of nodules consisted of maghemite. There was a slight transformation to hematite with time. The abundance of soil Fe nodules increased with terrace age on the five terraces studied (aged 65,000-226,000 yr). Scanning electron microscopy (SEM) revealed Fe-oxide-containing fungal hyphae throughout the nodules, including organic structures incorporating fine-grained Fe oxides. The fine-grained nature of the Fe oxides was substantiated by M??ssbauer spectroscopy. Our microscopic observations led to the hypothesis that the nodules in the Santa Cruz terrace soils are precipitated by fungi, perhaps as a strategy to sequester primary mineral grains for nutrient extraction. The fungal structures are fixed by the seasonal wetting and dry cycles and rounded through bioturbation. The organic structures are compacted by the degradation of fungal C with time. ?? Soil Science Society of America. All rights reserved.

  17. The association of thyroid nodule with non-iodized salt among Chinese children.

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    Weimin Xu

    Full Text Available The controversy that iodized salt may increase the risk of thyroid disorders has been aroused in China during the past decade. Most of studies focused on adult rather than children. We aimed to explore whether iodized salt was associated with an increased risk of thyroid nodule in Chinese children.The cross-sectional study was conducted in Hangzhou, China, in 2010. Iodized salt intake, urine iodine concentration (UIC and thyroid nodule (by ultrasonography were measured in 3026 children. The associations of iodized salt with thyroid nodule were evaluated using multiple logistic regression models.The prevalence of thyroid nodule was 10.59% among Chinese children. Girls (11.89% had higher prevalence of thyroid nodule than boys (9.26%. No significant association was observed between type of salt and thyroid nodule in pooled samples, boys and girls, respectively. Similar associations were observed between UIC and thyroid nodule. There was no significant association between milk consumption and thyroid nodule as well.The present study indicated that non-iodized salt may not increase the risk of thyroid nodules among Chinese children. Similar associations were observed between milk consumption, UIC and thyroid nodules.

  18. The Association of Thyroid Nodule with Non-Iodized Salt among Chinese Children

    Science.gov (United States)

    Liu, Hui; Huo, Liangliang; Huang, Yangmei; Jin, Xingyi; Deng, Jin; Zhu, Sujuan; Jin, Wen; Zhang, Shanchun; Yu, Yunxian

    2014-01-01

    Objective The controversy that iodized salt may increase the risk of thyroid disorders has been aroused in China during the past decade. Most of studies focused on adult rather than children. We aimed to explore whether iodized salt was associated with an increased risk of thyroid nodule in Chinese children. Methods The cross-sectional study was conducted in Hangzhou, China, in 2010. Iodized salt intake, urine iodine concentration (UIC) and thyroid nodule (by ultrasonography) were measured in 3026 children. The associations of iodized salt with thyroid nodule were evaluated using multiple logistic regression models. Results The prevalence of thyroid nodule was 10.59% among Chinese children. Girls (11.89%) had higher prevalence of thyroid nodule than boys (9.26%). No significant association was observed between type of salt and thyroid nodule in pooled samples, boys and girls, respectively. Similar associations were observed between UIC and thyroid nodule. There was no significant association between milk consumption and thyroid nodule as well. Conclusion The present study indicated that non-iodized salt may not increase the risk of thyroid nodules among Chinese children. Similar associations were observed between milk consumption, UIC and thyroid nodules. PMID:25068269

  19. Effect of Nitrate on Nodule and Root Growth of Soybean (Glycine max (L. Merr.

    Directory of Open Access Journals (Sweden)

    Akinori Saito

    2014-03-01

    Full Text Available The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °C or dark at 18 °C conditions. Photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer software. Nodule growth was depressed approximately 7 h after the addition of nitrate under light conditions. The nodule growth rate under dark conditions was almost half that under light conditions, and nodule growth was further suppressed by the addition of 5 mM nitrate. Similar results were observed for the extending growth rate of the primary root as those for nodule growth supplied with 5 mM nitrate under light/dark conditions. In contrast, the growth of lateral roots was promoted by the addition of 5 mM nitrate. The 2D-PAGE profiles of nodule protein showed similar patterns between the 0 and 5 mM nitrate treatments, which suggested that metabolic integrity may be maintained with the 5 mM nitrate treatment. Further studies are required to confirm whether light or temperature condition may give the primary effect on the growth of nodules and roots.

  20. Utilization of (15)NO3 (-) by nodulated soybean plants under conditions of root hypoxia.

    Science.gov (United States)

    Nunes Menolli Lanza, Luciana; Ferreira Lanza, Daniel Carlos; Sodek, Ladaslav

    2014-07-01

    Waterlogging of soils is common in nature. The low availability of oxygen under these conditions leads to hypoxia of the root system impairing the development and productivity of the plant. The presence of nitrate under flooding conditions is regarded as being beneficial towards tolerance to this stress. However, it is not known how nodulated soybean plants, cultivated in the absence of nitrate and therefore not metabolically adapted to this compound, would respond to nitrate under root hypoxia in comparison with non-nodulated plants grown on nitrate. A study was conducted with (15)N labelled nitrate supplied on waterlogging for a period of 48 h using both nodulated and non-nodulated plants of different physiological ages. Enrichment of N was found in roots and leaves with incorporation of the isotope in amino acids, although to a much smaller degree under hypoxia than normoxia. This demonstrates that nitrate is taken up under hypoxic conditions and assimilated into amino acids, although to a much lesser extent than for normoxia. The similar response obtained with nodulated and non-nodulated plants indicates the rapid metabolic adaptation of nodulated plants to the presence of nitrate under hypoxia. Enrichment of N in nodules was very much weaker with a distinct enrichment pattern of amino acids (especially asparagine) suggesting that labelling arose from a tissue source external to the nodule rather than through assimilation in the nodule itself.

  1. Outcome of hypovascular hepatic nodules with positive uptake of gadoxetic acid in patients with cirrhosis

    Energy Technology Data Exchange (ETDEWEB)

    Sano, Katsuhiro; Ichikawa, Tomoaki; Morisaka, Hiroyuki [University of Yamanashi, Department of Radiology, Chuo-City, Yamanashi (Japan); Saitama Medical University International Medical Center, Department of Diagnostic Radiology, Hidaka-City, Saitama (Japan); Motosugi, Utaroh; Ichikawa, Shintaro [University of Yamanashi, Department of Radiology, Chuo-City, Yamanashi (Japan); Enomoto, Nobuyuki [University of Yamanashi, First Department of Internal Medicine, Yamanashi (Japan); Matsuda, Masanori; Fujii, Hideki [University of Yamanashi, First Department of Surgery, Yamanashi (Japan)

    2017-02-15

    To evaluate the longitudinal risk to patients with cirrhosis of hypervascular hepatocellular carcinoma (HCC) developing from hypovascular hepatic nodules that show positive uptake of gadoxetic acid (hyperintensity) on hepatocyte phase images. In 69 patients, we evaluated findings from serial follow-up examinations of 633 hepatic nodules that appeared hypovascular and hyperintense on initial gadoxetic acid-enhanced magnetic resonance imaging (EOB-MRI) until the nodules demonstrated hypervascularity and were diagnosed as hypervascular HCC. Cox analyses were performed to identify risk factors for the development of hypervascular HCCs from the nodules. The median follow-up was 663 days (range, 110 to 1215 days). Hypervascular HCCs developed in six of the 633 nodules (0.9 %) in five of the 69 patients. The only independent risk factor, the nodule's initial maximum diameter of 10 mm or larger, demonstrated a hazard ratio of 1.25. The one-year risk of hypervascular HCC developing from a nodule was 0.44 %. The risk was significantly higher for nodules of larger diameter (1.31 %) than those smaller than 10 mm (0.10 %, p < 0.01). Hypervascular HCC rarely develops from hypovascular, hyperintense hepatic nodules. We observed low risk even for nodules of 10 mm and larger diameter at initial examination. (orig.)

  2. [Correlation between growth of callus and a number of nodule for pea Pisum sativum].

    Science.gov (United States)

    Petrov, Iu P

    2012-01-01

    The processes of nodulation and callusing were studied for pea Pisum sativum in a comparative aspect. Seven varieties of pea plants were used. The nodulation was characterized by the number of nodules and their mass per one plant. The frequency ratio of nodules of various weights was described by the Lorentz equation. The growth of callus was described using equation of the S-dependence. It has been shown that plants can produce maximal (optimum for nitrogen fixation) mass of nodules by an increase either in the nodules number or in the mass of each nodule. This feature is specific to the varieties of peas. It has been also found that the plants of the pea varieties, which have a large number of nodules, produce calluses of maximum size. Small calluses are characteristic of the varieties having plants with small amounts of large nodules. The data obtained has been interpreted on the assumption that the nodulation is underlined by both differentiation and proliferation, whereas the callusing is due only to the proliferation process.

  3. Characterization of rhizobial isolates nodulating Millettia pinnata in India.

    Science.gov (United States)

    Rasul, Abdul; Amalraj, E Leo Daniel; Praveen Kumar, G; Grover, Minakshi; Venkateswarlu, B

    2012-11-01

    Millettia pinnata (Synonym Pongamia pinnata) is a viable source of oil for the mushrooming biofuel industry, source for agroforestry, urban landscaping, and the bio-amelioration of degraded lands. It also helps in maintaining soil fertility through symbiotic nitrogen fixation. However, not much work is reported on classification and characterization of the rhizobia associated with this plant. In the present study, an attempt was made to isolate rhizobial strains nodulating Millettia from soils collected from southern regions of India. The isolates were characterized using numerical taxonomy, 16S rRNA gene sequencing, and cross nodulation ability. The results showed high phenotypic and genetic diversity among the rhizobia symbiotic with Millattia pinnata. The isolates formed five clusters at similarity level of 0.82 based on the results of numerical taxonomy. Results on 16S rRNA gene sequence analysis revealed that most microsymbionts of M. pinnata belonged to Rhizobium and Bradyrhizobium, which are closely related to Rhizobium sp., B. elkanii and B. yuanmingense. Among these isolates, some isolates could grow in a pH range of 4.0-10.0, some could tolerate a high salt concentration (3% NaCl) and could grow at a maximum temperature between 35 and 45 °C. M. pinnata formed nodules with diverse rhizobia in Indian soils. These results offered the first systematic information about the microsymbionts of M. pinnata grown in the soils from southern part of India. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  4. Quantitative imaging features to predict cancer status in lung nodules

    Science.gov (United States)

    Liu, Ying; Balagurunathan, Yoganand; Atwater, Thomas; Antic, Sanja; Li, Qian; Walker, Ronald; Smith, Gary T.; Massion, Pierre P.; Schabath, Matthew B.; Gillies, Robert J.

    2016-03-01

    Background: We propose a systematic methodology to quantify incidentally identified lung nodules based on observed radiological traits on a point scale. These quantitative traits classification model was used to predict cancer status. Materials and Methods: We used 102 patients' low dose computed tomography (LDCT) images for this study, 24 semantic traits were systematically scored from each image. We built a machine learning classifier in cross validation setting to find best predictive imaging features to differentiate malignant from benign lung nodules. Results: The best feature triplet to discriminate malignancy was based on long axis, concavity and lymphadenopathy with average AUC of 0.897 (Accuracy of 76.8%, Sensitivity of 64.3%, Specificity of 90%). A similar semantic triplet optimized on Sensitivity/Specificity (Youden's J index) included long axis, vascular convergence and lymphadenopathy which had an average AUC of 0.875 (Accuracy of 81.7%, Sensitivity of 76.2%, Specificity of 95%). Conclusions: Quantitative radiological image traits can differentiate malignant from benign lung nodules. These semantic features along with size measurement enhance the prediction accuracy.

  5. Drought stress responses in soybean roots and nodules

    Directory of Open Access Journals (Sweden)

    Karl Kunert

    2016-07-01

    Full Text Available Drought is considered to be a major threat to soybean production worldwide and yet our current understanding of the effects of drought on soybean productively is largely based on studies on above-ground traits. Although the roots and root nodules are important sensors of drought, the responses of these crucial organs and their drought tolerance features remain poorly characterized. The symbiotic interaction between soybean and rhizobia facilitates atmospheric nitrogen fixation, a process that provides essential nitrogen to support plant growth and development. Symbiotic nitrogen fixation is important for sustainable agriculture, as it sustains plant growth on nitrogen-poor soils and limits fertilizer use for crop nitrogen nutrition. Recent developments have been made in our understanding of the drought impact on soybean root architecture and nodule traits, as well as underpinning transcriptome, proteome and also emerging metabolome information, with a view to improve the selection of more drought-tolerant soybean cultivars and rhizobia in the future. We conclude that the direct screening of root and nodule traits in the field as well as identification of genes, proteins and also metabolites involved in such traits will be essential in order to gain a better understanding of the regulation of root architecture, bacteroid development and lifespan in relation to drought tolerance in soybean.

  6. Drought Stress Responses in Soybean Roots and Nodules.

    Science.gov (United States)

    Kunert, Karl J; Vorster, Barend J; Fenta, Berhanu A; Kibido, Tsholofelo; Dionisio, Giuseppe; Foyer, Christine H

    2016-01-01

    Drought is considered to be a major threat to soybean production worldwide and yet our current understanding of the effects of drought on soybean productively is largely based on studies on above-ground traits. Although the roots and root nodules are important sensors of drought, the responses of these crucial organs and their drought tolerance features remain poorly characterized. The symbiotic interaction between soybean and rhizobia facilitates atmospheric nitrogen fixation, a process that provides essential nitrogen to support plant growth and development. Symbiotic nitrogen fixation is important for sustainable agriculture, as it sustains plant growth on nitrogen-poor soils and limits fertilizer use for crop nitrogen nutrition. Recent developments have been made in our understanding of the drought impact on soybean root architecture and nodule traits, as well as underpinning transcriptome, proteome and also emerging metabolome information, with a view to improve the selection of more drought-tolerant soybean cultivars and rhizobia in the future. We conclude that the direct screening of root and nodule traits in the field as well as identification of genes, proteins and also metabolites involved in such traits will be essential in order to gain a better understanding of the regulation of root architecture, bacteroid development and lifespan in relation to drought tolerance in soybean.

  7. Lignin modification leads to increased nodule numbers in alfalfa.

    Science.gov (United States)

    Gallego-Giraldo, Lina; Bhattarai, Kishor; Pislariu, Catalina I; Nakashima, Jin; Jikumaru, Yusuke; Kamiya, Yuji; Udvardi, Michael K; Monteros, Maria J; Dixon, Richard A

    2014-03-01

    Reduction of lignin levels in the forage legume alfalfa (Medicago sativa) by down-regulation of the monolignol biosynthetic enzyme hydroxycinnamoyl coenzyme A:shikimate hydroxycinnamoyl transferase (HCT) results in strongly increased digestibility and processing ability of lignocellulose. However, these modifications are often also associated with dwarfing and other changes in plant growth. Given the importance of nitrogen fixation for legume growth, we evaluated the impact of constitutively targeted lignin modification on the belowground organs (roots and nodules) of alfalfa plants. HCT down-regulated alfalfa plants exhibit a striking reduction in root growth accompanied by an unexpected increase in nodule numbers when grown in the greenhouse or in the field. This phenotype is associated with increased levels of gibberellins and certain flavonoid compounds in roots. Although HCT down-regulation reduced biomass yields in both the greenhouse and field experiments, the impact on the allocation of nitrogen to shoots or roots was minimal. It is unlikely, therefore, that the altered growth phenotype of reduced-lignin alfalfa is a direct result of changes in nodulation or nitrogen fixation efficiency. Furthermore, HCT down-regulation has no measurable effect on carbon allocation to roots in either greenhouse or 3-year field trials.

  8. SUBFOVEAL NODULE IN COATS' DISEASE: Toward an Updated Classification Predicting Visual Prognosis.

    Science.gov (United States)

    Daruich, Alejandra L; Moulin, Alexandre P; Tran, Hoai V; Matet, Alexandre; Munier, Francis L

    2017-08-01

    To determine the prevalence, clinical characteristics and nature of subfoveal nodules in Coats' disease and the associated impact on the long-term visual outcome. Consecutive cases of Coats' disease with foveal exudation were retrospectively reviewed. The presence of a subfoveal nodule or macular fibrosis was recorded. Clinical characteristics, retinal imaging, and outcome were analyzed by comparative analysis. The histopathological description of an enucleated eye with subfoveal nodule was performed. Among 40 patients presenting unilateral Stage 2B or 3A1 Coats' disease, a subfoveal nodule was detected in 21 patients (52.5%). The median follow-up was 4.7 years. Nineteen patients (47.5%) did not present a subfoveal nodule. Three patients (15.8%) without subfoveal nodule and 21 patients (100%) with subfoveal nodule progressed to a macular fibrotic scar (P visual acuity was significantly worse in patients who presented a subfoveal nodule at diagnosis (P = 0.01). Of 18 cases with subfoveal nodule who underwent fluorescein angiography, retinal-retinal anastomosis and neovascularization were detected in 13 (72.2%) and 2 eyes (11.1%), respectively. Histopathological analysis of a subfoveal nodule revealed an aggregate of proteinaceous material including fibrin, spindle cells, macrophages, and pigmented cells. The presence of a subfoveal nodule at presentation is a predictive factor for macular fibrosis development and worse visual outcome in patients with Coats' disease. These observations suggest an updated classification introducing two subcategories within Stage 2B: without subfoveal nodule (Stage 2B1) and with subfoveal nodule (Stage 2B2).

  9. Acropetal Auxin Transport Inhibition Is Involved in Indeterminate But Not Determinate Nodule Formation

    Directory of Open Access Journals (Sweden)

    Jason L. P. Ng

    2018-02-01

    Full Text Available Legumes enter into a symbiotic relationship with nitrogen-fixing rhizobia, leading to nodule development. Two main types of nodules have been widely studied, indeterminate and determinate, which differ in the location of the first cell division in the root cortex, and persistency of the nodule meristem. Here, we compared the control of auxin transport, content, and response during the early stages of indeterminate and determinate nodule development in the model legumes Medicago truncatula and Lotus japonicus, respectively, to investigate whether differences in auxin transport control could explain the differences in the location of cortical cell divisions. While auxin responses were activated in dividing cortical cells during nodulation of both nodule types, auxin (indole-3-acetic acid content at the nodule initiation site was transiently increased in M. truncatula, but transiently reduced in L. japonicus. Root acropetal auxin transport was reduced in M. truncatula at the very start of nodule initiation, in contrast to a prolonged increase in acropetal auxin transport in L. japonicus. The auxin transport inhibitors 2,3,5-triiodobenzoic acid and 1-N-naphthylphthalamic acid (NPA only induced pseudonodules in legume species forming indeterminate nodules, but failed to elicit such structures in a range of species forming determinate nodules. The development of these pseudonodules in M. truncatula exhibited increased auxin responses in a small primordium formed from the pericycle, endodermis, and inner cortex, similar to rhizobia-induced nodule primordia. In contrast, a diffuse cortical auxin response and no associated cortical cell divisions were found in L. japonicus. Collectively, we hypothesize that a step of acropetal auxin transport inhibition is unique to the process of indeterminate nodule development, leading to auxin responses in pericycle, endodermis, and inner cortex cells, while increased auxin responses in outer cortex cells likely

  10. PII Overexpression in Lotus japonicus Affects Nodule Activity in Permissive Low-Nitrogen Conditions and Increases Nodule Numbers in High Nitrogen Treated Plants.

    Science.gov (United States)

    D'Apuzzo, Enrica; Valkov, Vladimir Totev; Parlati, Aurora; Omrane, Selim; Barbulova, Ani; Sainz, Maria Martha; Lentini, Marco; Esposito, Sergio; Rogato, Alessandra; Chiurazzi, Maurizio

    2015-04-01

    We report here the first characterization of a GLNB1 gene coding for the PII protein in leguminous plants. The main purpose of this work was the investigation of the possible roles played by this multifunctional protein in nodulation pathways. The Lotus japonicus LjGLB1 gene shows a significant transcriptional regulation during the light-dark cycle and different nitrogen availability, conditions that strongly affect nodule formation, development, and functioning. We also report analysis of the spatial profile of expression of LjGLB1 in root and nodule tissues and of the protein's subcellular localization. Transgenic L. japonicus lines overexpressing the PII protein were obtained and tested for the analysis of the symbiotic responses in different conditions. The uncoupling of PII from its native regulation affects nitrogenase activity and nodule polyamine content. Furthermore, our results suggest the involvement of PII in the signaling of the nitrogen nutritional status affecting the legumes' predisposition for nodule formation.

  11. Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa.

    Science.gov (United States)

    Steenkamp, Emma T; Stepkowski, Tomasz; Przymusiak, Anna; Botha, Wilhelm J; Law, Ian J

    2008-09-01

    Cowpea (Vigna unguiculata) and peanut (Arachis hypogaea) in southern Africa are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the identity of these bacteria, a collection of 22 isolates originating from the root nodules of both hosts in Botswana and South Africa was investigated using the combined sequences for the core genome genes rrs, recA, and glnII. These data separated the majority of the isolates into one of three unique lineages that most likely represent novel Bradyrhizobium species. Some isolates were also conspecific with B. yuanmingense and with B. elkanii, although none grouped with B. japonicum, B. canariense or B. liaoningense. To study the evolution of nodulation genes in these bacteria, the common nodulation gene, nodA, and host-specific nodulation genes, nodZ, noeE, and noeI, were analyzed. The nodA phylogeny showed that the cowpea and peanut Bradyrhizobium isolates represent various locally adapted groups or ecotypes that form part of Clade III of the seven known BradyrhizobiumnodA clades. This large and highly diverse clade comprises all strains from sub-Saharan Africa, as well as some originating from the Americas, Australia, Indonesia, China and Japan. Some similar groupings were supported by the other nodulation genes, although the overall phylogenies for the nodulation genes were incongruent with that inferred from the core genome genes, suggesting that horizontal gene transfer significantly influences the evolution of cowpea and peanut root-nodule bacteria. Furthermore, identification of the nodZ, noeI, and noeE genes in the isolates tested indicates that African Bradyrhizobium species may produce highly decorated nodulation factors, which potentially represent an important adaptation enabling nodulation of a great variety of legumes inhabiting the African continent.

  12. Role of Computer Aided Diagnosis (CAD) in the detection of pulmonary nodules on 64 row multi detector computed tomography.

    Science.gov (United States)

    Prakashini, K; Babu, Satish; Rajgopal, K V; Kokila, K Raja

    2016-01-01

    To determine the overall performance of an existing CAD algorithm with thin-section computed tomography (CT) in the detection of pulmonary nodules and to evaluate detection sensitivity at a varying range of nodule density, size, and location. A cross-sectional prospective study was conducted on 20 patients with 322 suspected nodules who underwent diagnostic chest imaging using 64-row multi-detector CT. The examinations were evaluated on reconstructed images of 1.4 mm thickness and 0.7 mm interval. Detection of pulmonary nodules, initially by a radiologist of 2 years experience (RAD) and later by CAD lung nodule software was assessed. Then, CAD nodule candidates were accepted or rejected accordingly. Detected nodules were classified based on their size, density, and location. The performance of the RAD and CAD system was compared with the gold standard that is true nodules confirmed by consensus of senior RAD and CAD together. The overall sensitivity and false-positive (FP) rate of CAD software was calculated. Of the 322 suspected nodules, 221 were classified as true nodules on the consensus of senior RAD and CAD together. Of the true nodules, the RAD detected 206 (93.2%) and 202 (91.4%) by the CAD. CAD and RAD together picked up more number of nodules than either CAD or RAD alone. Overall sensitivity for nodule detection with the CAD program was 91.4%, and FP detection per patient was 5.5%. The CAD showed comparatively higher sensitivity for nodules of size 4-10 mm (93.4%) and nodules in hilar (100%) and central (96.5%) location when compared to RAD's performance. CAD performance was high in detecting pulmonary nodules including the small size and low-density nodules. CAD even with relatively high FP rate, assists and improves RAD's performance as a second reader, especially for nodules located in the central and hilar region and for small nodules by saving RADs time.

  13. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

    OpenAIRE

    Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

    2016-01-01

    Legumes are known as pioneer plants colonizing marginal soils, and as enhancers of the nutritional status in cultivated soils. This beneficial activity has been explained by their capacity to engage in symbiotic relationship with nitrogen-fixing rhizobia. We performed a community profiling analysis of Lotus japonicus wild type and mutants to investigate the role of the nodulation pathway on the structure of the root-associated bacterial microbiota. We found that several bacterial orders were ...

  14. NPR1 protein regulates pathogenic and symbiotic interactions between Rhizobium and legumes and non-legumes.

    Science.gov (United States)

    Peleg-Grossman, Smadar; Golani, Yael; Kaye, Yuval; Melamed-Book, Naomi; Levine, Alex

    2009-12-21

    Legumes are unique in their ability to establish symbiotic interaction with rhizobacteria from Rhizobium genus, which provide them with available nitrogen. Nodulation factors (NFs) produced by Rhizobium initiate legume root hair deformation and curling that entrap the bacteria, and allow it to grow inside the plant. In contrast, legumes and non-legumes activate defense responses when inoculated with pathogenic bacteria. One major defense pathway is mediated by salicylic acid (SA). SA is sensed and transduced to downstream defense components by a redox-regulated protein called NPR1. We used Arabidopsis mutants in SA defense pathway to test the role of NPR1 in symbiotic interactions. Inoculation of Sinorhizobium meliloti or purified NF on Medicago truncatula or nim1/npr1 A. thaliana mutants induced root hair deformation and transcription of early and late nodulins. Application of S. meliloti or NF on M. truncatula or A. thaliana roots also induced a strong oxidative burst that lasted much longer than in plants inoculated with pathogenic or mutualistic bacteria. Transient overexpression of NPR1 in M. truncatula suppressed root hair curling, while inhibition of NPR1 expression by RNAi accelerated curling. We show that, while NPR1 has a positive effect on pathogen resistance, it has a negative effect on symbiotic interactions, by inhibiting root hair deformation and nodulin expression. Our results also show that basic plant responses to Rhizobium inoculation are conserved in legumes and non-legumes.

  15. NPR1 protein regulates pathogenic and symbiotic interactions between Rhizobium and legumes and non-legumes.

    Directory of Open Access Journals (Sweden)

    Smadar Peleg-Grossman

    Full Text Available BACKGROUND: Legumes are unique in their ability to establish symbiotic interaction with rhizobacteria from Rhizobium genus, which provide them with available nitrogen. Nodulation factors (NFs produced by Rhizobium initiate legume root hair deformation and curling that entrap the bacteria, and allow it to grow inside the plant. In contrast, legumes and non-legumes activate defense responses when inoculated with pathogenic bacteria. One major defense pathway is mediated by salicylic acid (SA. SA is sensed and transduced to downstream defense components by a redox-regulated protein called NPR1. METHODOLOGY/PRINCIPAL FINDINGS: We used Arabidopsis mutants in SA defense pathway to test the role of NPR1 in symbiotic interactions. Inoculation of Sinorhizobium meliloti or purified NF on Medicago truncatula or nim1/npr1 A. thaliana mutants induced root hair deformation and transcription of early and late nodulins. Application of S. meliloti or NF on M. truncatula or A. thaliana roots also induced a strong oxidative burst that lasted much longer than in plants inoculated with pathogenic or mutualistic bacteria. Transient overexpression of NPR1 in M. truncatula suppressed root hair curling, while inhibition of NPR1 expression by RNAi accelerated curling. CONCLUSIONS/SIGNIFICANCE: We show that, while NPR1 has a positive effect on pathogen resistance, it has a negative effect on symbiotic interactions, by inhibiting root hair deformation and nodulin expression. Our results also show that basic plant responses to Rhizobium inoculation are conserved in legumes and non-legumes.

  16. Influence of the in-plane artefact in chest tomosynthesis on pulmonary nodule size measurements

    International Nuclear Information System (INIS)

    Soederman, Christina; Allansdotter Johnsson, Aase; Vikgren, Jenny; Rossi Norrlund, Rauni; Molnar, David; Svalkvist, Angelica; Maansson, Lars Gunnar; Baath, Magnus

    2016-01-01

    The aim of the present study was to investigate how the in-plane artefact present in the scan direction around structures in tomosynthesis images should be managed when measuring the size of nodules in chest tomosynthesis images in order to achieve acceptable measurement accuracy. Data from measurements, performed by radiologists, of the longest diameter of artificial nodules inserted in chest tomosynthesis images were used. The association between the measurement error and the direction of the longest nodule diameter, relative to the scan direction, was evaluated using the Kendall rank correlation coefficient. All of the radiologists had chosen to not include the artefact in the measurements. Significant association between measurement error and the direction of the longest diameter was found for nodules larger than 12 mm, which indicates that, for these nodules, there is a risk of underestimating the nodule size if the in-plane artefact is omitted from manual diameter measurements. (authors)

  17. The Lotus japonicus ndx gene family is involved in nodule function and maintenance

    DEFF Research Database (Denmark)

    Grønlund, Mette; Gustafsen, Camilla; Jensen, Dorthe Bødker

    2003-01-01

    To elucidate the function of the ndx homeobox genes during the Rhizobium-legume symbiosis, two Lotus japonicus ndr genes were expressed in the antisense orientation under the control of the nodule-expressed promoter Psenod12 in transgenic Lotus japonicus plants. Many of the transformants obtained...... segregated into plants that failed to sustain proper development and maintenance of root nodules concomitant with down-regulation of the two ndx genes. The root nodules were actively fixing nitrogen 3 weeks after inoculation, but the plants exhibited a stunted growth phenotype. The nodules on such antisense...... supplied to the plants in which the two ndx genes are down-regulated. The results presented here, indicate that the ndx genes play a role in the development of structural nodule features, required for proper gas diffusion into the nodule and/or transport of the assimilated nitrogen to the plant....

  18. Ground-Glass Opacity Lung Nodules in the Era of Lung Cancer CT Screening

    DEFF Research Database (Denmark)

    Pedersen, Jesper Holst; Saghir, Zaigham; Wille, Mathilde Marie Winkler

    2016-01-01

    The advent of computed tomography screening for lung cancer will increase the incidence of ground-glass opacity (GGO) nodules detected and referred for diagnostic evaluation and management. GGO nodules remain a diagnostic challenge; therefore, a more systematic approach is necessary to ensure...... correct diagnosis and optimal management. Here we present the latest advances in the radiologic imaging and pathology of GGO nodules, demonstrating that radiologic features are increasingly predictive of the pathology of GGO nodules. We review the current guidelines from the Fleischner Society......, the National Comprehensive Cancer Network, and the British Thoracic Society. In addition, we discuss the management and follow-up of GGO nodules in the light of experience from screening trials. Minimally invasive tissue biopsies and the marking of GGO nodules for surgery are new and rapidly developing fields...

  19. A pulmonary nodule view system for the Lung Image Database Consortium (LIDC).

    Science.gov (United States)

    Lin, Hongli; Chen, Zhencheng; Wang, Weisheng

    2011-09-01

    The aim of this study was to develop a pulmonary nodule viewing system to visualize and retrieve data from the Lung Image Database Consortium. The pulmonary nodule viewing system, developed using Microsoft C++ and the .NET 2.0 Framework, is composed of a clinical information integrator, a nodule viewer, a search engine, and a data model. A pulmonary nodule viewing system using Lung Image Database Consortium data for computer-aided diagnosis research and training purpose was developed. The pulmonary nodule viewing system can be used to build a pulmonary nodule database for computer-aided diagnosis research and medical education. It can also be used to view and retrieve large data sets efficiently. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

  20. Discrimination method of large log-likelihood study in differential diagnosis of pulmonary diffuse mild micro-nodule

    International Nuclear Information System (INIS)

    Chen Budong; Ma Daqing; He Wen; Tang Hongqu; Qian Linxue; Zhou Ronglin

    2001-01-01

    Objective: To analyze HRCT and thin-slice CT scan findings in 150 patients with pulmonary diffuse mild micro-nodule, and to find the features with the purpose of identifying random micro-nodule, peri-lymphatic micro-nodule, and centrilobular micro-nodule. Methods: The useful features i 150 patients with pulmonary diffuse mild micro-nodule were translated into scores by means of discrimination method of large log-likelihood to identify the micro-nodular category. Results: The accuracy of diagnosis was 94.0% for random micro-nodule, 76.0% for peri-lymphatic micro-nodule, and 90.0% for centrilobular micro-nodule. Conclusion: HRCT and thin-slice CT scans were helpful in differential diagnosis of pulmonary diffuse mild micro-nodule. The discrimination method of large log-likelihood was propitious to diagnosis and differential diagnosis

  1. Differences between endocrinologists and endocrine surgeons in management of the solitary thyroid nodule

    DEFF Research Database (Denmark)

    Walsh, John P; Ryan, Simon A; Lisewski, Dean

    2007-01-01

    BACKGROUND: It is not known whether management of the solitary thyroid nodule differs between endocrinologists and endocrine surgeons. METHODS: A questionnaire containing a hypothetical case (a 42-year-old euthyroid woman with a 2-x-3-cm solitary thyroid nodule) and 13 clinical variations was sent...... Thyroid Association members (predominantly endocrinologists) demonstrated considerable international differences in management. CONCLUSION: There are clinically significant differences between Australian endocrinologists and endocrine surgeons in management of the solitary thyroid nodule...

  2. Diversity and nitrogen fixation efficiency of rhizobia isolated from nodules of Centrolobium paraense

    OpenAIRE

    Baraúna, Alexandre Cardoso; Silva, Krisle da; Pereira, Gilmara Maria Duarte; Kaminski, Paulo Emílio; Perin, Liamara; Zilli, Jerri Edson

    2014-01-01

    The objective of this work was to isolate and characterize rhizobia from nodules of Centrolobium paraense and to evaluate their symbiotic efficiency. Soil samples collected from four sites of the Roraima Cerrado, Brazil, were used to cultivate C. paraense in order to obtain nodules. Isolates (178) were obtained from 334 nodules after cultivation on medium 79. Twenty-five isolates belonging to six morphological groups were authenticated using Vigna unguiculata and they were characterized by 16...

  3. Hyperfunction thyroid nodules: Their risk for becoming or being associated with thyroid cancers

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun Sun; Kim, Ji Hoon; Na, Dong Gyu; Paeng, Jin Chul; Min, Hye Sook; Choi, Seung Hong; Sohn, Chul Ho; Chang, Ki Hyun [Seoul National University Hospital, Seoul (Korea, Republic of)

    2013-08-15

    To retrospectively evaluate the risk of thyroid cancer in patients with hyperfunctioning thyroid nodules through ultrasonographic-pathologic analysis. Institutional review board approval was obtained and informed consent was waived. From 2003 to 2007, 107 patients consecutively presented with hot spots on thyroid scans and low serum thyroid-stimulating hormone levels. Among them, 32 patients who had undergone thyroid ultrasonography were analyzed in this study. Thyroid nodules depicted on ultrasonography were classified based on size and categorized as benign, indeterminate, or suspicious malignant nodules according to ultrasonographic findings. The thyroid nodules were determined as either hyperfunctioning or coexisting nodules and were then correlated with pathologic results. In 32 patients, 42 hyperfunctioning nodules (mean number per patient, 1.31; range, 1-6) were observed on thyroid scans and 68 coexisting nodules (mean, 2.13; range, 0-7) were observed on ultrasonography. Twenty-five patients (78.1%) had at least one hyperfunctioning (n = 17, 53.1%) or coexisting (n = 16, 50.0%) nodule that showed a suspicious malignant feature larger than 5 mm (n = 8, 25.0%), or an indeterminate feature 1 cm or greater (n = 20, 62.5%) in diameter, which could have been indicated by using fine needle aspiration (FNA). Seven patients were proven to have 11 thyroid cancers in 3 hyperfunctioning and 8 coexisting nodules. All of these had at least one thyroid cancer, which could have been indicated by using FNA. The estimated minimal risk of thyroid cancer was 6.5% (7/107). Patients with hyperfunctioning nodules may not be safe from thyroid cancer because hyperfunctioning nodules can coexist with thyroid cancer nodules. To screen out these cancers, ultrasonography should be performed.

  4. 3-D Analysis of Graphite Nodules in Ductile Cast Iron Using FIB-SEM

    DEFF Research Database (Denmark)

    D'Angelo, Luca; Jespersen, Freja N.; MacDonald, A. Nicole

    Ductile cast iron samples were analysed in a Focused Ion Beam Scanning Electron Microscope, FIB-SEM. The focussed ion beam was used to carefully remove layers of the graphite nodules to reveal internal structures in the nodules. The sample preparation and milling procedure for sectioning graphite...... nodules is described and ef-fects of preparation methods discussed. It was found that nodules contain different types of inclusions. These were analysed for chemical composition and crystallography using energy dispersive spectrometry (EDS) and electron back-scatter patterns (EBSP). Location of inclusions...

  5. A COMPREHENSIVE FRAMEWORK FOR AUTOMATIC DETECTION OF PULMONARY NODULES IN LUNG CT IMAGES

    Directory of Open Access Journals (Sweden)

    Mehdi Alilou

    2014-03-01

    Full Text Available Solitary pulmonary nodules may indicate an early stage of lung cancer. Hence, the early detection of nodules is the most efficient way for saving the lives of patients. The aim of this paper is to present a comprehensive Computer Aided Diagnosis (CADx framework for detection of the lung nodules in computed tomography images. The four major components of the developed framework are lung segmentation, identification of candidate nodules, classification and visualization. The process starts with segmentation of lung regions from the thorax. Then, inside the segmented lung regions, candidate nodules are identified using an approach based on multiple thresholds followed by morphological opening and 3D region growing algorithm. Finally, a combination of a rule-based procedure and support vector machine classifier (SVM is utilized to classify the candidate nodules. The proposed CADx method was validated on CT images of 60 patients, containing the total of 211 nodules, selected from the publicly available Lung Image Database Consortium (LIDC image dataset. Comparing to the other state of the art methods, the proposed framework demonstrated acceptable detection performance (Sensitivity: 0.80; Fp/Scan: 3.9. Furthermore, we visualize a range of anatomical structures including the 3D lung structure and the segmented nodules along with the Maximum Intensity Projection (MIP volume rendering method that will enable the radiologists to accurately and easily estimate the distance between the lung structures and the nodules which are frequently difficult at best to recognize from CT images.

  6. The role of nodules in the tolerance of common bean to iron deficiency.

    Science.gov (United States)

    Slatni, Tarek; Ben Salah, Imen; Kouas, Saber; Abdelly, Chedly

    2014-05-01

    Iron is vital for the establishment and function of symbiotic root nodules of legumes. Although abundant in the environment, Fe is often a limiting nutrient for plant growth due to its low solubility and availability in some soils. We have studied the mechanism of iron uptake in the root nodules of common bean to evaluate the role of nodules in physiological responses to iron deficiency. Based on experiments using full or partial submergence of nodulated roots in the nutrient solution, our results show that the nodules were affected only slightly under iron deficiency, especially when the nodules were submerged in nutrient solution in the tolerant cultivar. In addition, fully submerged root nodules showed enhanced acidification of the nutrient solution and showed higher ferric chelate reductase activity than that of partially submerged roots in plants cultivated under Fe deficiency. The main results obtained in this work suggest that in addition to preferential Fe allocation from the root system to the nodules, this symbiotic organ probably develops some mechanisms to respond to iron deficiency. These mechanisms were implied especially in nodule Fe absorption efficiency and in the ability of this organ to take up Fe directly from the medium.

  7. Characteristics of bacteroids in indeterminate nodules of the leguminous tree Leucaena glauca.

    Science.gov (United States)

    Ishihara, Hironobu; Koriyama, Hiroki; Osawa, Atsushi; Zehirov, Grigor; Yamaura, Masatoshi; Kucho, Ken-ichi; Abe, Mikiko; Higashi, Shiro; Kondorosi, Eva; Mergaert, Peter; Uchiumi, Toshiki

    2011-01-01

    Rhizobia establish symbiosis with legumes. Bacteroids in indeterminate nodules of Inverted Repeat Lacking Clade (IRLC) legumes undergo terminal differentiation caused by Nodule-specific Cysteine-Rich peptides (NCRs). Microscopic observations of bacteroids and the detection of NCRs in indeterminate nodules of the non-IRLC legume Leucaena glauca were performed. A portion of the bacteroids showed moderate cell elongation, loss of membrane integrity, and multiple nucleoids. The symbiosome contained multiple bacteroids and NCR-like peptides were not detectable. These results indicate that bacteroid differentiation in L. glauca is different from that in IRLC legumes although both hosts form indeterminate nodules.

  8. A salt stress-responsive cytokinin receptor homologue isolated from Medicago sativa nodules.

    Science.gov (United States)

    Coba de la Peña, Teodoro; Cárcamo, Claudia B; Almonacid, Luis; Zaballos, Angel; Lucas, M Mercedes; Balomenos, Dimitrios; Pueyo, José J

    2008-03-01

    A new cytokinin receptor homologue, MsHK1, was isolated from Medicago sativa root nodules. MsHK1 expression was induced in alfalfa seedlings by exogenous application of the cytokinin trans-zeatin. Transcript accumulation was detected in different plant organs. MsHK1 expression was induced by salt stress in alfalfa roots, leaves and nodules, and transcript accumulation in the vascular bundles pointed to a putative role in osmosensing for MsHK1 and/or other close cytokinin receptor homologues. Expression in the meristem and the invasion zone of the nodule suggest a role for cytokinin receptors in cytokinin sensing during nodule cell division and differentiation.

  9. Transport and partitioning of CO2 fixed by root nodules of ureide and amide producing legumes

    International Nuclear Information System (INIS)

    Vance, C.P.; Boylan, K.L.M.; Maxwell, C.A.; Heichel, G.H.; Hardman, L.L.

    1985-01-01

    Nodulated and denodulated roots of adzuki bean (Vigna angularis), soybean (Glycine max), and alfalfa (Medicago sativa) were exposed to 14 CO 2 to investigate the contribution of nodule CO 2 fixation to assimilation and transport of fixed nitrogen. The distribution of radioactivity in xylem sap and partitioning of carbon fixed by nodules to the whole plant were measured. Radioactivity in the xylem sap of nodulated soybean and adzuki bean was located primarily (70 to 87%) in the acid fraction while the basic (amino acid) fraction contained 10 to 22%. In contrast radioactivity in the xylem sap of nodulated alfalfa was primarily in amino acids with about 20% in organic acids. Total ureide concentration was 8.1, 4.7, and 0.0 micromoles per milliliter xylem sap for soybean, adzuki bean, and alfalfa, respectively. While the major nitrogen transport products in soybeans and adzuki beans are ureides, this class of metabolites contained less than 20% of the the total radioactivity. When nodules of plants were removed, radioactivity in xylem sap decreased by 90% or more. Pulse-chase experiments indicated that CO 2 fixed by nodules was rapidly transported to shoots and incorporated into acid stable constituents. The data are consistent with a role for nodule CO 2 fixation providing carbon for the assimilation and transport of fixed nitrogen in amide-based legumes. In contrast, CO 2 fixation by nodules of ureide transporting legumes appears to contribute little to assimilation and transport of fixed nitrogen. 19 references, 2 figures, 5 tables

  10. Inter-relationship between nuclei and gross characteristics of manganese nodules, Central Indian Ocean Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Sarkar, C.; Iyer, S.D.; Hazra, S.

    type, cannon ball-like and irregular nodules are not uncommon (Fig. 3). Many of these shapes are similar to nodules recovered in other oceans (Glasby et al., 1983; Friedrich et al., 1983). Generally, the small sized nodules are spheroidal... the selected CIOB nodules, we observed that altered basalt comprises 56.15%, clay (mainly palagonite) 17.54%, fresh basalt 12.3%, sharks’ teeth 3.51%, pumice 2.34%, poly-nucleated 5.26 % and the remaining 2.92 % are unidentified (Figs. 6, 7; Tables 2, 3...

  11. Resistance to nodulation of cv. Afghanistan peas is overcome by nodX, which mediates an O-acetylation of the Rhizobium leguminosarum lipo-oligosaccharide nodulation factor.

    Science.gov (United States)

    Firmin, J L; Wilson, K E; Carlson, R W; Davies, A E; Downie, J A

    1993-10-01

    Only some strains of Rhizobium leguminosarum biovar viciae can efficiently nodulate varieties of peas such as cv. Afghanistan, which carry a recessive allele that blocks efficient nodulation by most western isolates of R.I. viciae. One strain (TOM) which can nodulate cv. Afghanistan peas has a gene (nodX) that is required to overcome the nodulation resistance. Strain TOM makes significantly lower amounts of lipo-oligosaccharide nodulation factors than other strains of R.I. viciae and this effect appears to be due to lower levels of nod gene induction. These nodulation factors are similar to those from other R.I. viciae strains in that they consist of an oligomer of four or five beta 1-4-linked N-acetylglucosamine residues in which the terminal non-reducing glucosamine carries an O-acetyl group and a C18:4 or C18:1 N-acyl group. However, one of the nodulation factors made by strain TOM differs from the factors made by other strains of R.I. viciae in that it carries an O-acetyl group on the C-6 of the reducing N-acetylglucosamine residue. This acetylation is NodX-dependent and the pentameric nodulation factor is acetylated on the reducing N-acetylglucosamine residue whereas the tetrameric nodulation factor is not. Although the nodL gene product is also an O-acetyl transferase (it O-acetylates the C-6 of the terminal non-reducing glucosamine), there is very little similarity between the amino acid sequences of these two acetyl transferases.

  12. Fast-neutron activation analysis of manganese nodules

    International Nuclear Information System (INIS)

    Michaelis, W.; Fanger, H.U.; Mueller, A.; Pepelnik, R.

    1976-01-01

    The present paper describes the development of a new nuclear method that allows rapid determinations of the most relevant metals Ni and Cu without sample treatment, thus being particularly suited for quasi-continuous elemental analyses in mining and processing. The measurement is based on fast-neutron activation using Cockcroft-Walton generators, sealed neutron tubes or, possibly, (α,n)-type natural sources. Fast-neutron activation of manganese nodules is dominated by the (n,p)-reactions on Si, Al, Fe; the (n,α)-reaction on Mn and the (n,2n)-reaction on Cu. By choosing appropriate irradiation and cooling periods gamma-ray activities with comparatively simple spectral distributions are induced. From these spectra the Mn/Fe ratio in the nodules can be determined without the elaborate procedures usually required in absolute methods for eliminating systematic errors from fluctuations in sample and/or irradiation parameters. It is connected with the absolute Ni and Cu contents via well-known geochemical correlations which according to a lot of statistical data apply to quite different deposits and nodule types in the Pacific. Using these correlations the determination of the most important metals reduces to the evaluation of a peak area ratio. Measurements of the neutron flux distribution and the apparent sample density are unnecessary. The simple structure of the spectra allows the application of detectors with modest energy resolution, e.g. scintillation counters which can be manufactured as ruggedized crystal assemblies with great resistance to thermal and mechanical shock. The method is described in detail and possible interference, in particular from thermal and epithermal neutrons, are discussed. (orig.) [de

  13. Piezogenic pedal nodules of young children and their parents

    Directory of Open Access Journals (Sweden)

    Piotr Brzezinski

    2013-01-01

    Full Text Available Introduction: Skin of atlets foot is open on constant effect of disadvantageous outword factors, which could be reason of illnesses in this area. Very ofen incidence disease is Piezogenic Foot Nodules (PN These papules represent herniations of subcutaneous fat through the collagen matrix of the reticular dermis. Suggests that as many as 10% to 20% of the population may be affected with both symptomatic and asymptomatic lesions. Painful piezogenic papules are reported more frequently in women than in man. Among athletes they appear mainly at the marathon runners and valleybol players. Trauma may also initiate the formation of pedal papules. These are soft, skin collored, typically asymptomatic, medial heel papules and nodules, appear on the side of the heel, ussualy the medial aspect, when the subject is standing and disappear when weight is taken off the foot. Papules may be painful when there is herniation of fat into the dermis with a resultant reduction in dermal thickness. They could concern one or both feet. Ussually there are plural changes. There is no satisfactory medical or surgical treatment.Aim: The aim of work is presentation family occurrence of PN.Material and methods: Research concerned 50 children (girls and boys in age about 5,5 years.Results: Incidence of PN observed at 16 % children and 22.06% in check up group (5 children. In children and parents group 100% changes concerned heels. Pain reportered only 4 parents (5,88%.Conclusions: Appearance skin changes during fat ill on Piezogenic Nodules is connected with doing more activity. Painful papules can limit participation in sports and may affect occupational activity.

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

    Science.gov (United States)

    Staehelin, Christian; Krishnan, Hari B

    2015-09-15

    Rhizobia are nitrogen-fixing bacteria that establish a nodule symbiosis with legumes. Nodule formation depends on signals and surface determinants produced by both symbiotic partners. Among them, rhizobial Nops (nodulation outer proteins) play a crucial symbiotic role in many strain-host combinations. Nops are defined as proteins secreted via a rhizobial T3SS (type III secretion system). Functional T3SSs have been characterized in many rhizobial strains. Nops have been identified using various genetic, biochemical, proteomic, genomic and experimental approaches. Certain Nops represent extracellular components of the T3SS, which are visible in electron micrographs as bacterial surface appendages called T3 (type III) pili. Other Nops are T3 effector proteins that can be translocated into plant cells. Rhizobial T3 effectors manipulate cellular processes in host cells to suppress plant defence responses against rhizobia and to promote symbiosis-related processes. Accordingly, mutant strains deficient in synthesis or secretion of T3 effectors show reduced symbiotic properties on certain host plants. On the other hand, direct or indirect recognition of T3 effectors by plant cells expressing specific R (resistance) proteins can result in effector triggered defence responses that negatively affect rhizobial infection. Hence Nops are double-edged swords that may promote establishment of symbiosis with one legume (symbiotic factors) and impair symbiotic processes when bacteria are inoculated on another legume species (asymbiotic factors). In the present review, we provide an overview of our current understanding of Nops. We summarize their symbiotic effects, their biochemical properties and their possible modes of action. Finally, we discuss future perspectives in the field of T3 effector research. © 2015 Authors; published by Portland Press Limited.

  15. Rheumatoid arthritis and pulmonary nodules: An unexpected final diagnosis.

    Science.gov (United States)

    Zurita Prada, Pablo Antonio; Urrego Laurín, Claudia Lía; Assyaaton Bobo, Sow; Faré García, Regina; Estrada Trigueros, Graciliano; Gallardo Romero, José Manuel; Borrego Pintado, Maria Henar

    We report the case of a 50-year-old female smoker with an 11-year history of seropositive rheumatoid arthritis (rheumatoid factor and anti-cyclic citrullinated peptide antibodies) receiving triple therapy. She developed pulmonary nodules diagnosed as Langerhans cell histiocytosis by lung biopsy. We found no reported cases of the coexistence of these two diseases. Smoking abstinence led to radiologic resolution without modifying the immunosuppressive therapy. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

  16. Surgical resection of highly suspicious pulmonary nodules without a tissue diagnosis

    International Nuclear Information System (INIS)

    Heo, Eun-Young; Lee, Kyung-Won; Jheon, Sanghoon; Lee, Jae-Ho; Lee, Choon-Taek; Yoon, Ho-II

    2011-01-01

    The safety and efficacy of surgical resection of lung nodule without tissue diagnosis is controversial. We evaluated direct surgical resection of highly suspicious pulmonary nodules and the clinical and radiological predictors of malignancy. Retrospective analyses were performed on 113 patients who underwent surgical resection without prior tissue diagnosis for highly suspicious pulmonary nodules. Clinical and radiological characteristics were compared between histologically proven benign and malignant nodules after resection. Total costs, length of hospitalization and waiting time to surgery were compared with those of patients who had tissue diagnosis prior to surgery. Among 280 patients with pulmonary nodules suspicious for lung cancer, 113 (40.4%) underwent operation without prior tissue diagnosis. Lung nodules were diagnosed as malignant in 96 (85%) of the 113 patients. Except for forced expiratory volume in 1 s, clinical characteristics were not significantly different according to the pathologic results. Forty-five (90%) of 50 patients with ground-glass opacity nodules had a malignancy. Mixed ground-glass opacity, bubble lucency, irregular margin and larger size correlated with malignancy in ground-glass opacity nodules (P<0.05). Fifty-one (81%) of 67 patients with solid nodules had a malignancy. Spiculation, pre-contrast attenuation and contrast enhancement significantly correlated with malignancy in solid nodules (P<0.05). Surgical resection without tissue diagnosis significantly decreased total costs, hospital stay and waiting time (P<0.05). Direct surgical resection of highly suspicious pulmonary nodules can be a valid procedure. However, careful patient selection and further investigations are required to justify direct surgical resection. (author)

  17. Effect of local background anatomical patterns on the detection of subtle lung nodules in chest radiographs

    Science.gov (United States)

    Samei, Ehsan; Flynn, Michael J.; Eyler, William R.; Peterson, Edward

    1998-04-01

    Anatomical noise in chest radiography, created by the projection of anatomical features in the thorax such as ribs and pulmonary vessels, greatly influences the detection of subtle lung nodules in chest radiographs. Detection may be hindered by 1) the 'global' statistical characteristics of the background in relation to the signal associated withthe nodule, and/or 2) the interference of the 'local' background pattern with the nodule signal. This investigation aimed at assessing the influence of the latter process in the detection of subtle lung nodules. Six 8 X 8 cm images were extracted from the lung regions o six digital chest radiographs of normal patients from our clinic. Simulated nodules emulating the radiographic characteristics of subtle tissue-equivalent lesions ranging in size from 3.2 to 6.4 mm were numerically superimposed on the images. For each of the six lung images, a set of thirty-one processed images were produced, six containing no nodule, and the remaining 25 containing single nodules of five different sizes placed at five different locations within 6 mm of the center. The variation in location allowed different local background patterns to overlay the nodules. An observer detection study was then performed using 14 experienced radiologists. The observer data were analyzed to determine the variation in detectability with nodule location for all five sizes of the nodules. The preliminary results indicate that the variation in detectability of a nodule due to the influence of its local background surroundings is equivalent to that caused by changing its CD product by a factor of 4.45.

  18. Three Dimensional Volumetric Analysis of Solid Pulmonary Nodules on Chest CT: 
Cancer Risk Assessment

    Directory of Open Access Journals (Sweden)

    Mengqi LI

    2016-05-01

    Full Text Available Background and objective The management of pulmonary nodules relies on cancer risk assessment, in which the only widely accepted criterion is diameter. The development of volumetric computed tomography (CT and three-dimensional (3D software enhances the clarity in displaying the nodules’ characteristics. This study evaluated the values of the nodules’ volume and 3D morphological characteristics (edge, shape and location in cancer risk assessment. Methods The CT data of 200 pulmonary nodules were retrospectively evaluated using 3D volumetric software. The malignancy or benignity of all the nodules was confirmed by pathology, histology or follow up (>2 years. Logistic regression analysis was performed to calculate the odds ratios (ORs of the 3D margin (smooth, lobulated or spiculated/irregular, shape (spherical or non-spherical, location (purely intraparenchymal, juxtavascular or pleural-attached, and nodule volume in cancer risk assessment for total and sub-centimeter nodules. The receiver operating characteristic (ROC curve was employed to determine the optimal threshold for the nodule volume. Results Out of 200 pulmonary nodules, 78 were malignant, whereas 122 were benign. The Logistic regression analysis showed that the volume (OR=3.3; P0.05. ROC analysis showed that the optimal threshold for malignancy was 666 mm³. For sub-centimeter nodules, the 3D margin was the only valuable predictive factor of malignancy (OR=60.5, 75.0; P=0.003, 0.007. Conclusion The volume and 3D margin are important factors considered to assess the cancer risk of pulmonary nodules. Volumes larger than 666 mm³ can be determined as high risk for pulmonary nodules; by contrast, nodules with lobulated, spiculated, or irregular margin present a high malignancy probability.

  19. Paediatric CT: the effects of increasing image noise on pulmonary nodule detection

    International Nuclear Information System (INIS)

    Punwani, Shonit; Davies, Warren; Greenhalgh, Rebecca; Humphries, Paul; Zhang, Jie

    2008-01-01

    A radiation dose of any magnitude can produce a detrimental effect manifesting as an increased risk of cancer. Cancer development may be delayed for many years following radiation exposure. Minimizing radiation dose in children is particularly important. However, reducing the dose can reduce image quality and may, therefore, hinder lesion detection. We investigated the effects of reducing the image signal-to-noise ratio (SNR) on CT lung nodule detection for a range of nodule sizes. A simulated nodule was placed at the periphery of the lung on an axial CT slice using image editing software. Multiple copies of the manipulated image were saved with various levels of superimposed noise. The image creation process was repeated for a range of nodule sizes. For a given nodule size, output images were read independently by four Fellows of The Royal College of Radiologists. The overall sensitivities in detecting nodules for the SNR ranges 0.8-0.99, 1-1.49, and 1.5-2.35 were 40.5%, 77.3% and 90.3%, respectively, and the specificities were 47.9%, 73.3% and 75%, respectively. The sensitivity for detecting lung nodules increased with nodule size and increasing SNR. There was 100% sensitivity for the detection of nodules of 4-10 mm in diameter at SNRs greater than 1.5. Reducing medical radiation doses in children is of paramount importance. For chest CT examinations this may be counterbalanced by reduced sensitivity and specificity combined with an increased uncertainty of pulmonary nodule detection. This study demonstrates that pulmonary nodules of 4 mm and greater in diameter can be detected with 100% sensitivity provided that the perceived image SNR is greater than 1.5. (orig.)

  20. The value of HIC1 and SIRT1 expression levels in thyroid nodule for assessing benign or malignant nodules

    Directory of Open Access Journals (Sweden)

    Chuan-Hua Fang

    2016-09-01

    Full Text Available Objective: To study the value of HIC1 and SIRT1 expression levels in thyroid nodule for assessing benign or malignant nodules. Method: 70 cases of surgically removed thyroid cancer tissue samples were collected as pathology group, 70 cases of corresponding para-carcinoma tissue specimens were collected as control group, immunohistochemistry was used to detect HIC1 and SIRT1 protein expression levels, and fluorescence quantitative PCR was used to detect the mRNA expression levels of HIC1 and SIRT1 as well as OXTR, CDH1, RASSF1A, TIMP3, MMP13, S100A4, CCNG2 and MK. Results: HIC1 expression levels in thyroid carcinoma tissue of pathology group were significantly lower than those of control group while SIRT1 expression levels were significantly higher than those of control group; compared with thyroid cancer tissue with TNM I-II stage, negative ductal infiltration and negative lymph node metastasis, HIC1 expression levels significantly decreased while SIRT1 expression levels significantly increased in thyroid cancer tissue with TNM III-IV stage, positive ductal infiltration and positive lymph node metastasis; in thyroid cancer tissue with positive HIC1 expression, OXTR, CDH1, RASSF1A and TIMP3 expression levels were significantly higher than those in thyroid cancer tissue with negative HIC1 expression; in thyroid cancer tissue with positive SIRT1 expression, MMP13, S100A4, CCNG2 and MK expression levels were significantly higher than those in thyroid cancer tissue with negative SIRT1 expression. Conclusion: HIC1 expression deletion and SIRT1 expression increase in thyroid nodule tissue are associated with the occurrence and development of thyroid carcinoma, and methylation and deacetylation may be epigenetic mechanism of HIC1 and SIRT1 to regulate cell proliferation, invasion and angiogenesis.