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Cooperative Action of Rhizobium meliloti Nodulation and Infection Mutants during the Process of Forming Mixed Infected Alfalfa Nodules.

Alfalfa plants co-inoculated with Rhizobium meliloti nodulation (Nod-) and infection mutants deficient in exopolysaccharide production (Inf-EPS-) formed mixed infected nodules that were capable of fixing atmospheric nitrogen. The formation of infected nodules was dependent on close contact between the inoculation partners. When the partners were separated by a filter, empty Fix- nodules were formed, suggesting that infection thread formation in alfalfa is dependent on signals from the nodulation and infection genes. In mixed infected nodules, both nodulation and infection mutants colonized the plant cells and differentiated into bacteroids. The formation of bacteroids was not dependent on cell-to-cell contact between the mutants. Immunogold/silver staining revealed that the ratio of the two mutants varied considerably in colonized plant cells following mixed inoculation. The introduction of an additional nif/fix mutation into one of the inoculation partners did not abolish nitrogen fixation in mixed infected nodules. The expression of nif D::lacZ fusions additionally demonstrated that mutations in the nodulation and infection genes did not prevent the nif genes from being expressed in the mutant bacteroids.

Journal Article↗

Resistance to nodulation of cv. Afghanistan peas is overcome by nodX, which mediates an O-acetylation of the Rhizobium leguminosarum lipo-oligosaccharide nodulation factor.

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.

Acetylation↗

Lipopolysaccharide profiles from nodules as markers of bradyrhizobium strains nodulating wild legumes.

To develop the use of electrophoretic lipopolysaccharide profiles for Bradyrhizobium strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. The electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. To assess the reliability of using lipopolysaccharide profiling performed with individual nodules for studying the diversity and microdistribution of the rhizobia nodulating wild shrub legumes, we used a population of Adenocarpus foliolosus seedlings. We obtained 75 different profiles from the 147 nodules studied. There was no dominant profile in the sample, and a plant with different nodules generally produced different profiles. Electrophoresis of legume root nodules proved to be a fast and discriminating technique for determining the diversity of a bradyrhizobial population, although it did not allow the genetic relationships among the nodulating strains to be studied.

Journal Article↗

Outcome of 51 nonmalignant nodules in the liver: usefulness of aspiration cytology for diagnosis of dysplastic nodules.

Pathologic diagnostic criteria for intrahepatic nonmalignant nodules using needle biopsy are controversial. To evaluate the cytodiagnostic criteria for dysplastic nodules using aspiration biopsy, a follow-up study of nonmalignant nodules was performed. Fifty-one intrahepatic nodules diagnosed histologically and cytologically as nonmalignant using an aspiration biopsy in 39 patients were followed up without treatment. The outcomes of the nodules were investigated using the Kaplan-Meier method and Cox's multivariate analysis. The cumulative rates of development to HCC at the 2nd year were 0%, 18%, and 53% in the non-dysplastic nodules, the low-grade dysplastic nodules, and the high-grade dysplastic nodules, respectively; and significant differences were seen among them (P= 0.0001). Multivariate analysis showed that cytologic grade was a significant risk factor for development to HCC (P=0.020). In conclusion, aspiration cytology was useful for diagnosis of the dysplastic nodules to predict risks of development to HCC.

Adult↗

[Diagnostic value of echography in the study of thyroid nodules. Ultrasonographic and histological findings on 103 "cold" nodules].

This study examines the accuracy of ultrasonic scanning in the recognition of malignancy in 103 "cold" thyroid nodules. All nodules underwent to surgical ablation and to histopathological examination. 10 nodules were cistic, 72 solid and 21 mixed cistic-solid on echography. None of the cistic nodules showed malignant disease while six carcinomas were present in solid nodules and one (a papillary cancer) in a mixed cistic-solid lesion. However we were unable to find echographic abnormalities pathognomonic for malignancy. Only in one case (an undifferentiated carcinoma which involved adjacent blood vessels) the diagnosis of malignant tumour was made before operation; in the other cases the echo patterns of the carcinomatous nodules were similar to those observed in benign nodules. Similar ultrasonic findings were also seen in the various types of thyroid cancer (3 follicular, 2 papillary, 1 medullary, 1 undifferentiated) a part the papillary carcinoma which appeared as cistic-solid lesion. Our data seem to limit the diagnostic value of echography in the detection of malignant thyroid nodules, nevertheless they confirm the benignancy of echografically cistic nodules.

Adenoma↗

[Digital analysis of pulmonary nodules--potential usefulness of computer-aided diagnosis for differentiation of benign from malignant nodules].

Digital analysis of 80 plain chest radiographs was done to differentiate benign from malignant pulmonary nodules. Each of 80 radiographs had a solitary pulmonary nodule, of which 40 were benign and the other 40 were malignant. Radiographic features of nodules were visually evaluated. Frequencies of the radiographic features described below were significantly different between benign and malignant nodules: irregular shape, vague density, well-defined contour, spicular formation, and vascular convergene. To digitally evaluate the density characteristics, two kinds of concentric circular windows were used, to allow analysis of intra-nodular, marginal and surrounding regions of the nodules. Seventeen digital parameters were obtained by computerized analysis with the windows. There were significant differences in six digital parameters; three of density gradient (one of intra-nodular and two of marginal regions), one DCF-N (directional contrast filter for nodule) output of intra-nodular region, and two of density entropy values of intra-nodular and surrounding regions. Density gradient parameters of marginal regions are believed to represent the features of nodular shape and spicula formation. With these six parameters, 70% of benign nodules and 85% of malignant nodules were correctly discriminated. These results suggest that computer-aided diagnosis may be used to differentiate benign from malignant nodules.

Diagnosis, Computer-Assisted↗

Fractal analysis of small peripheral pulmonary nodules in thin-section CT: evaluation of the lung-nodule interfaces.

OBJECTIVES: To analyze the lung-nodule interfaces on small peripheral pulmonary nodules (<2 cm) in thin-section CT (HRCT) images with fractal analysis. METHODS: Thin-section CT images from 70 patients with bronchogenic carcinomas (61 adenocarcinomas and 9 squamous cell carcinomas) and 47 patients with benign pulmonary nodules (23 hamartomas, 13 organizing pneumonias, and 11 tuberculomas) were used. For calculation of fractal dimensions (FDs), the authors used a box-counting method for binary- and gray-scale images of nodules. FD(two-dimensional [2D]) was an FD obtained from the binary image, and FD(three-dimensional [3D]) was an FD obtained from the gray-scale image. RESULTS: The FD(2D)s of hamartomas were smaller than those of other nodules ( < 0.05). The FD(3D)s obtained from the gray-scale images of organizing pneumonias and tuberculomas were greater than those of bronchogenic carcinomas ( < 0.0001) and hamartomas ( < 0.0001). In bronchogenic carcinomas, FD(3D)s of adenocarcinomas were greater than those of squamous cell carcinomas ( < 0.05). CONCLUSIONS: Fractal dimensions reflect the characteristics of the lung-nodule interfaces of small peripheral pulmonary nodules. The FD(2D)s revealed the irregularities of the contours. On the other hand, FD(3D)s revealed the complexities of the heterogeneous textures. With use of FD(2D) and FD(3D), it may be possible to distinguish bronchogenic carcinomas from benign pulmonary nodules. Moreover, FD(3D) may make it possible to distinguish between adenocarcinomas and squamous cell carcinomas.

Adenocarcinoma↗

Development of a digital image database for chest radiographs with and without a lung nodule: receiver operating characteristic analysis of radiologists' detection of pulmonary nodules.

OBJECTIVE: We developed a digital image database (www.macnet.or.jp/jsrt2/cdrom_nodules.html ) of 247 chest radiographs with and without a lung nodule. The aim of this study was to investigate the characteristics of image databases for potential use in various digital image research projects. Radiologists' detection of solitary pulmonary nodules included in the database was evaluated using a receiver operating characteristic (ROC) analysis. MATERIALS AND METHODS: One hundred and fifty-four conventional chest radiographs with a lung nodule and 93 radiographs without a nodule were selected from 14 medical centers and were digitized by a laser digitizer with a 2048 x 2048 matrix size (0.175-mm pixels) and a 12-bit gray scale. Lung nodule images were classified into five groups according to the degrees of subtlety shown. The observations of 20 participating radiologists were subjected to ROC analysis for detecting solitary pulmonary nodules. Experimental results (areas under the curve, Az) obtained from observer studies were used for characterization of five groups of lung nodules with different degrees of subtlety. RESULTS: ROC analysis showed that the database included a wide range of various nodules yielding Az values from 0.574 to 0.991 for the five categories of cases for different degrees of subtlety. CONCLUSION: This database can be useful for many purposes, including research, education, quality assurance, and other demonstrations.

Adult↗

The solitary pulmonary nodule on chest radiography: can we really tell if the nodule is calcified?

OBJECTIVE: This study was designed to assess the ability of radiologists to accurately detect calcification within a solitary pulmonary nodule with chest radiography. MATERIALS AND METHODS: Thirty-five solitary pulmonary nodules that were examined by both posteroanterior and lateral chest radiography and on thin-section CT were retrospectively identified. Fourteen radiologists blinded to the results of CT assessed the nodules for the presence or absence of calcification using chest radiographs alone. The radiologists then assigned one of six values on the basis of their confidence in that assessment. The accuracy and confidence values for each nodule were analyzed on the basis of the presence or absence of calcification as seen on CT. Receiver operating characteristic (ROC) curves were generated. RESULTS: The positive predictive value of a "definitely calcified" assessment was 0.93. Combining all levels of radiologists' confidence, the sensitivity of the chest radiograph in the detection of calcium was 0.50 and the specificity was 0.87. There was no difference in the confidence levels reported between the calcified and noncalcified nodules, and there was no correlation of nodule size with accuracy or confidence level. CONCLUSION: The ability of radiologists to detect calcium in a solitary pulmonary nodule by chest radiography was low, as defined by the ROC data. Of the "definitely calcified" nodules, up to 7% may not be calcified and may be potentially malignant. Without documentation of long-term stability, a low threshold for recommending CT may be appropriate.

Aged↗

Soybean nodule sucrose synthase (nodulin-100): further analysis of its phosphorylation using recombinant and authentic root-nodule enzymes.

Sucrose synthase (SS) is a known phosphoserine-containing enzyme in legume root nodules and various other plant "sink" tissues. In order to begin to investigate the possible physiological significance of this posttranslational modification, we have cloned a full-length soybean nodule SS (nodulin-100) cDNA and overexpressed it in Escherichia coli. Authentic nodule SS and recombinant wild-type and mutant forms of the enzyme were purified and characterized. We document that a conserved serine near the N-terminus (Ser(11)) is the primary phosphorylation site for a nodule Ca(2+)-dependent protein kinase (CDPK) in vitro. Related tryptic digestion and mass spectral analyses indicated that this target residue was also phosphorylated in planta in authentic nodulin-100. In addition, a secondary phosphorylation site(s) in recombinant nodule SS was implicated given that all active mutant enzyme forms (S11A, S11D, S11C, and N-terminal truncation between Ala(2) and Arg(13)) were phosphorylated, albeit weakly, by the CDPK. This secondary site(s) likely resides between Glu(14) and Met(193) as evidenced by CNBr cleavage and phosphopeptide mapping. Phosphorylation of the recombinant and authentic nodule Ser(11) enzymes in vitro by the nodule CDPK had no major effect on the sucrose-cleavage activity and/or kinetic properties. However, phosphorylation decreased the apparent surface hydrophobicity of the recombinant wild-type enzyme, suggesting that this covalent modification could potentially play some role in the documented partitioning of nodulin-100 between the nodule symbiosome/plasma membranes and cytosol in planta.

Amino Acid Sequence↗

Analysis of pss genes of Rhizobium leguminosarum required for exopolysaccharide synthesis and nodulation of peas: their primary structure and their interaction with psi and other nodulation genes.

Strains of Rhizobium leguminosarum (R.l.) biovar viciae containing pss mutations fail to make the acidic exopolysaccharides (EPS) and are unable to nodulate peas. It was found that they also failed to nodulate Vicia hirsuta, another host of this biovar. When peas were co-inoculated with pss mutant derivatives of a strain of R.l. by viciae containing a sym plasmid plus a cured strain lacking a sym plasmid (and which is thus Nod-, but for different reasons) but which makes the acidic EPS, normal numbers of nodules were formed, the majority of which failed to fix nitrogen (the occasional Fix+ nodules were presumably induced by strains that arose as a result of genetic exchange between cells of the two inoculants in the rhizosphere). Bacteria from the Fix- nodules contained, exclusively, the strain lacking its sym plasmid. When pss mutant strains were co-inoculated with a Nod- strain with a mutation in the regulatory gene nodD (which is on the sym plasmid pRL1JI), normal numbers of Fix+ nodules were formed, all of which were occupied solely by the nodD mutant strain. Since a mutation in nodD abolishes activation of other nod genes required for early stages of infection, these nod genes appear to be dispensable for subsequent stages in nodule development. Recombinant plasmids, containing cloned pss genes, overcame the inhibitory effects of psi, a gene which when cloned in the plasmid vector pKT230, inhibits both EPS production and nodulation ability. Determination of the sequence of the pss DNA showed that one, or perhaps two, genes are required for correcting strains that either carry pss mutations or contain multi-copy psi.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗

Sesbania herbacea-Rhizobium huautlense Nodulation in Flooded Soils and Comparative Characterization of S. herbacea-Nodulating Rhizobia in Different Environments.

The nodulation of S. herbacea was compared under flooded and non-flooded conditions in two different soils. One soil was from a flooded field in Sierra de Huautla, the native habitat of this legume, while the other soil was from a well-drained field in Cuernavaca, where rhizobia were found to nodulate the introduced S. herbacea plants. Nodulation of the plants was completely eliminated by flooding in the Cuernavaca soil, whereas nodules were obtained in the same soil under non-flooded conditions. In contrast, nodules were formed in Huautla soil under both flooded and non-flooded conditions. Most isolates, except isolate HS2, from Huautla soil and water were identified as R. huautlense by colony morphology, growth rate, PCR-RFLP of 16S rRNA genes, MLEE, cellular plasmid contents, and RFLP of nifH and nodDAB genes. Isolate HS2 was identified as Mesorhizobium sp. Isolates from Cuernavaca soil were different from R. huautlense in many aspects and were classified into five rDNA types within the genera Mesorhizobium, Rhizobium, and Sinorhizobium by PCR-RFLP of 16S rRNA genes. R. huautlense is a water Rhizobium species. Growth by denitrification under oxygen limitation or with ethanol was observed for R. huautlense bacteria but not for the isolates from Cuernavaca. In an interstrain nodulation competitive assay under both flooded and non-flooded conditions, R. huautlense strain S02 completely inhibited the nodulation of Mesorhizobium sp. Sn2, an isolate from Cuernavaca. From these results, we conclude that R. huautlense has the unique ability to nodulate S. herbacea not only in flooded soils, but in non-flooded soils as well.

Journal Article↗

Developmental regulation of nodule-specific genes in alfalfa root nodules.

We have cloned alfalfa nodule-specific cDNAs that code for leghemoglobin (Lb), glutamine synthetase (GS), and three unidentified nodulins. Hybrid-select translation of nodule RNA followed by 2-D gel electrophoresis showed that the Lb-specific cDNA corresponded to at least four Lb species of 12 kDa. One of the unidentified cDNA clones (N-32/34) corresponded to at least five polypeptides of 32-34 kDa; a second unidentified cDNA clone (N-14) corresponded to an individual polypeptide of 14 kDa. The in vitro translation product(s) of the RNA hybrid selected by the third unidentified cDNA clone (N-22) formed a single band at 22 kDa on a one-dimensional gel. Northern and dot blot analyses of RNA isolated from wild-type nodules and from defective nodules elicited by a variety of Rhizobium meliloti mutants showed that 1) RNAs corresponding to the Lb, nodule-specific GS, and three unidentified nodulins were coordinately expressed during the course of nodule development, and 2) all five nodulins were expressed in Fix- nodules that contained infection threads and bacteroids but were not expressed in nodules that lacked infection threads and intracellular rhizobia.

Base Sequence↗

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

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.

Adaptation, Physiological↗

Glycine-rich proteins encoded by a nodule-specific gene family are implicated in different stages of symbiotic nodule development in Medicago spp.

Four genes encoding small proteins with significantly high glycine content have been identified from root nodules of Medicago sativa. All of these proteins as well as their Medicago truncatula homologues carried an amino terminal signal peptide and a glycine-rich carboxy terminal domain. All except nodGRP3 lacked the characteristic repeat structure described for cell wall and stress response-related glycine-rich proteins (GRP). Expression of these GRP genes was undetectable in flower, leaf, stem, and hypocotyl cells, whereas expression was highly induced during root nodule development, suggesting that GRP genes act as nodulins. Moreover, none of these nodule-expressed GRP genes were activated by hormones or stress treatments, which are inducers of many other GRPs. In Rhizobium-free spontaneous nodules and in nodules induced by a noninfective mutant strain of Sinorhizobium meliloti, all these genes were repressed, while they were induced in Fix- nodules, unaffected in bacterial infection, but halted in bacteroid differentiation. These results demonstrated that bacterial infection but not bacteroid differentiation is required for the induction of the nodule-specific GRP genes. Differences in kinetics and localization of gene activation as well as in the primary structure of proteins suggest nonredundant roles for these GRPs in nodule organogenesis.

Amino Acid Sequence↗

Simulation of lung nodules for nodule detection studies.

Two techniques for simulating lung nodules in nodule detection studies were evaluated. In one technique, radiographs were obtained with plastic beads placed on the surface of a chest phantom to simulate lung nodules. In the second technique, the same plastic beads were radiographed against a uniform background, and their radiographic images were then superimposed photographically onto a radiograph of the same chest phantom. Nodule detection rates determined by four different film readers were significantly different for films prepared by the two different techniques. The differences in detection rates are explained by differences in nodule contrast due to film sensitometric characteristics and scattered radiation effects. Photographic superpositioning does not mimic these effects accurately, as they affect clinical chest films. For this reason, it is suggested that nodule simulation films prepared by the photographic superpositioning technique cannot be used to predict nodule detection rates for clinical chest radiography. Other aspects of lung nodule simulation techniques also are discussed.

Absorptiometry, Photon↗

Oxygen-Induced Membrane Depolarizations in Legume Root Nodules (Possible Evidence for an Osmoelectrical Mechanism Controlling Nodule Gas Permeability).

Various stresses trigger rapid and reversible decreases in the O2 permeability (PO) of legume root nodules. Several possible mechanisms have been proposed, but no supporting data have previously been presented that meet the requirements for both rapidity and reversibility. Stomatal regulation of gas permeability in leaves involves electrically driven fluxes of inorganic osmoticants, so we investigated the possibility of a somewhat similar mechanism in nodules. We used microelectrodes to monitor membrane potential in intact, attached nodules of Glycine max, Medicago sativa, Lotus corniculatus, and Trifolium repens while controlling external O2 concentration and, in the case of G. max, measuring PO with a nodule oximeter. A 1- to 2-min exposure to 100 kPa O2 was found to induce rapid and reversible membrane depolarizations in nodules of each species. This depolarization (which, to our knowledge, is unique to nodules) is accompanied by reversible decreases in PO in G. max nodules. An osmoelectrical mechanism for control of nodule gas permeability, consistent with these data, is presented.

Journal Article↗

Carbon Dioxide Fixation by Lupin Root Nodules: I. Characterization, Association with Phosphoenolpyruvate Carboxylase, and Correlation with Nitrogen Fixation during Nodule Development.

In vivo CO(2) fixation and in vitro phosphoenolpyruvate (PEP) carboxylase levels have been measured in lupin (Lupinus angustifolius L.) root nodules of various ages. Both activities were greater in nodule tissue than in either primary or secondary root tissue, and increased about 3-fold with the onset of N(2) fixation. PEP carboxylase activity was predominantly located in the bacteroid-containing zone of mature nodules, but purified bacteroids contained no activity. Partially purified PEP carboxylases from nodules, roots, and leaves were identical in a number of kinetic parameters. Both in vivo CO(2) fixation activity and in vitro PEP carboxylase activity were significantly correlated with nodule acetylene reduction activity during nodule development. The maximum rate of in vivo CO(2) fixation in mature nodules was 7.9 nmol hour(-1) mg fresh weight(-1), similar to rates of N(2) fixation and reported values for amino acid translocation.The results suggest that the oxaloacetete used as the primary "carbon skeleton" acceptor for ammonia assimilation and amino acid synthesis in lupin nodules is provided via the PEP carboxylase reaction rather than through the tricarboxylic acid cycle. The source of PEP is presumably glycolysis, while the major source of CO(2) is inferred to be respiration.

Journal Article↗