Phenogenetic profile and agronomic contribution of Azospirillum argentinense Az39T, a reference strain for the South American inoculant industry.

Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20-38 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance.

Unraveling Azospirillum's colonization ability through microbiological and molecular evidence.

It is known that members of the bacterial genus Azospirillum can promote the growth of a great variety of plants, an ability harnessed by the industry to create bioproducts aimed to enhance the yield of economically relevant crops. Its versatile metabolism allows this bacterium to adapt to numerous environments, from optimal to extreme or highly polluted. The fact of having been isolated from soil and rhizosphere samples collected worldwide and many other habitats proves its remarkable ubiquity. Azospirillum rhizospheric and endophytic lifestyles are governed by several mechanisms, leading to efficient niche colonization. These mechanisms include cell aggregation and biofilm formation, motility, chemotaxis, phytohormone and other signaling molecules production, and cell-to-cell communication, in turn, involved in regulating Azospirillum interactions with the surrounding microbial community. Despite being infrequently mentioned in metagenomics studies after its introduction as an inoculant, an increasing number of studies detected Azospirillum through molecular tools (mostly 16S rRNA sequencing) as part of diverse, even unexpected, microbiomes. This review focuses on Azospirillum traceability and the performance of the available methods, both classical and molecular. An overview of Azospirillum occurrence in diverse microbiomes and the less-known features explaining its notorious ability to colonize niches and prevail in multiple environments is provided.

Day and blue light modify growth, cell physiology and indole-3-acetic acid production of Azospirillum brasilense Az39 under planktonic growth conditions.

AIM: In this work, we evaluated the effects of light on growth, cell physiology and stress response of Azospirillum brasilense Az39, a non-photosynthetic rhizobacteria, under planktonic growth conditions. METHODS AND RESULTS: Exponential cultures of Az39 were exposed to blue (BL), red (RL) and daylight (DL) or maintained in darkness for 24, 48 and 72 h. The biomass production and indole 3-acetic acid (IAA) biosynthesis increased by exposition to DL. Conversely, BL decreased IAA concentration through a direct effect on the molecule. The DL increased superoxide dismutase activity, hydrogen peroxide and thiobarbituric acid reactive substances levels, but the last one was also increased by BL. Both DL and BL increased cell aggregation but only BL increased biofilm formation. CONCLUSIONS: We demonstrated that both BL and DL are stress effectors for A. brasilense Az39 under planktonic growth conditions. The DL increased biomass production, IAA biosynthesis and bacterial response to stress, whereas BL induced cell aggregation and biofilms formation, but decreased the IAA concentration by photooxidation. SIGNIFICANCE AND IMPACT OF THE STUDY: Blue light and DL changes growth capacity, cell physiology and plant growth promotion ability of A. brasilense Az39 and these changes could be considered to improve the production and functionality of biofertilizers.

Azospirillum brasilense Az39, a model rhizobacterium with AHL quorum-quenching capacity.

AIMS: The aim of this research was to analyse the quorum-sensing (QS) and quorum-quenching (QQ) mechanisms based on N-acyl-l-homoserine lactones (AHLs) in Azospirillum brasilense Az39, a strain with remarkable capacity to benefit a wide range of crops under agronomic conditions. METHODS AND RESULTS: We performed an in silico and in vitro analysis of the quorum mechanisms in A. brasilense Az39. The results obtained in vitro using the reporter strains Chromobacterium violaceum and Agrobacterium tumefaciens and liquid chromatography coupled with mass-mass spectrometry analysis showed that although Az39 does not produce AHL molecules, it is capable of degrading them by at least two hypothetical enzymes identified by bioinformatics approach, associated with the bacterial cell. In Az39 cultures supplemented with 500 nmol l-1 of the C3 unsubstituted AHLs (C4, C6, C8, C10, C12, C14), AHL levels were lower than in noninoculated LB media controls. Similar results were observed upon the addition of AHLs with hydroxy (OH-) and keto (oxo-) substitutions in C3. These results not only demonstrate the ability of Az39 to degrade AHLs. They also show the wide spectrum of molecules that can be degraded by this bacterium. CONCLUSIONS: Although A. brasilense Az39 is a silent bacterium unable to produce AHL signals, it is able to interrupt the communications between other bacteria and/or plants by a QQ activity. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report confirming by unequivocal methodology the ability of A. brasilense, one of the most agriculturally used benefic bacteria around the world, to degrade AHLs by a QQ mechanism.

Clinical comparison between simple laminectomy and laminectomy plus posterior instrumentation in surgical treatment of cervical myelopathy.

BACKGROUND: Posterior stabilization in patients treated with laminectomy for spondylotic cervical myelopathy is still a debate. Despite both being reported in literature by several authors, some controversies still exist. The aim of this study is to compare clinical and radiological outcomes in patients treated with laminectomy or laminectomy with posterior stabilization. MATERIAL AND METHODS: We retrospectively evaluated 42 patients affected by cervical myelopathy (mean age 70.43 ± 5.03 years), 19 treated with laminectomy (group A) and 23 with laminectomy and posterior instrumentation (group B). Neurological status was assessed with Nurick scale, pain with VAS and radiological parameters with C2-C7 SVA, T1 slope and C2-C7 lordosis, clinical function with modified Japanese Orthopaedic Association score (JOA). Also, surgery time and blood loss were recorded. Student's t test was used for continuous variables, while Kruskal-Wallis test was used for categorical values. RESULTS: No differences were found in postoperative Nurick scale (p = 0.587), VAS (p = 0.62), mJOA (p = 0.197) and T1 slope (p = 0.559), while laminectomy with fusion showed better postoperative cervical lordosis (p = 0.007) and C2-C7 SVA (p < 0.00001), but higher blood loss (p < 0.00001) and surgical time (p < 0.00001). Both groups showed better Nurick scale (p = 0.00017 for group A and p = 0.00081 for group B), VAS (p = 0.02 for group A and p = 0.046 for group B) and mJOA (p < 0.00001 for both groups) than preoperative values. CONCLUSIONS: Both treatments are a valuable choice, offering some benefits and disadvantages against each other. Each procedure must be carefully evaluated on the basis of patients' general status, preoperative pain, signs of instability and potential benefits from cervical alignment correction.

Extended lymphadenectomy in elderly and/or highly co-morbid gastric cancer patients: A retrospective multicenter study.

BACKGROUND: Gastrectomy with extended lymphadenectomy is considered the gold standard treatment for advanced gastric cancer, with no age- or comorbidity-related limitations. We evaluated the safety and efficacy of curative gastrectomy with extended nodal dissection, verifying survival in elderly and highly co-morbid patients. METHODS: In a retrospective multicenter study, we examined 1322 non-metastatic gastric-cancer patients that underwent curative gastrectomy with D2 versus D1 lymphadenectomy from January 2000 to December 2009. Postoperative complications, overall survival (OS), and disease-specific survival (DSS) according to age and the Charlson Comorbidity Score were analyzed in relation to the extent of lymphadenectomy. RESULTS: Postoperative morbidity was 30.4%. Complications were more frequent in highly co-morbid elderly patients, and, although general morbidity rates after D2 and D1 lymphadenectomy were similar (29.9% and 33.2%, respectively), they increased following D2 in highly co-morbid elderly patients (39.6%). D2-lymphadenectomy significantly improved 5-year OS and DSS (48.0% vs. 37.6% in D1, p < 0.001 and 72.6% vs. 58.1% in D1, p < 0.001, respectively) in all patients. In elderly patients, this benefit was present only in 5-year DSS. D2 nodal dissection induced better 5-year OS and DSS rates in elderly patients with positive nodes (29.7% vs. 21.2% in D1, p = 0.008 and 47.5% vs. 30.6% in D1, p = 0.001, respectively), although it was present only in DSS when highly co-morbid elderly patients were considered. CONCLUSION: Extended lymphadenectomy confirmed better survival rates in gastric cancer patients. Due to high postoperative complication rate and no significant improvement of the OS, D1 lymphadenectomy should be considered in elderly and/or highly co-morbid gastric cancer patients.

Gastric GISTs: Analysis of c-Kit, PDGFRA and BRAF mutations in relation to prognosis and clinical pathological characteristics of patients - A GIRCG study.

BACKGROUND: Gastric gastrointestinal stromal tumors (GISTs) represent a subgroup of GISTs with a better prognosis than those located in other areas. In this retrospective study we performed a molecular characterization of a large series of patients with gastric GISTs in relation to clinical-pathological characteristics and prognosis. METHODS: DNA was extracted from paraffin-embedded sections from 221 gastric GIST patients submitted to surgery. Exons 9, 11, 13 and 17 of KIT, exons 12 and 18 of PDGFRA and exons 11 and 15 of BRAF were analyzed by direct sequencing. Cox regression analysis adjusted for clinical-pathological factors was performed to evaluate KIT and PDGFRA mutations in relation to the composite endpoint of relapse or death. RESULTS: KIT and PDGFRA mutations were observed in 119 (53.8%) and 56 (25.3%) patients, respectively, whereas 46 (20.8%) patients had wild type (wt) disease. Univariable analyses showed that a high Miettinen risk category and the presence of ulceration and KIT deletions were associated with increased risk of relapse or death (p < 0.001; p = 0.0389 and p = 0.002, respectively). After adjusting for Miettinen risk score, KIT deletions remained an independent prognostic factor (HRadj = 2.65, 95% CI [1.15-6.13], p = 0.023). Moreover, KIT deletions in exon 11 codons 557, 558 or 559 were associated with a higher risk of relapse or death than wt tumors (HRadj = 3.29 95% CI [1.64-6.64], p = 0.001). CONCLUSIONS: KIT deletions in exon 11, especially those involving codons 557, 558 or 559, were correlated with a more aggressive gastric GIST phenotype and increased risk of relapse or death.

Multiple 3D inversion recovery imaging for volume T1 mapping of the heart.

In this article, a three-dimensional inversion recovery sequence was optimized with the aim of generating in vivo volume T(1) maps of the heart using a 1.5-T MR system. Acquisitions were performed before and after gadolinium diethylenetriamine penta-acetic acid (Gd-DTPA) administration in one patient with hypertrophic cardiomyopathy and in two healthy volunteers. Data were acquired with a multishot fast field echo readout using both ECG and respiratory triggers. A dedicated phantom, composed of four solutions with different T(1) values, was positioned on the subjects' thoracic region to perform patient-specific calibration. Pixel based T(1) maps were calculated with a custom Matlab(®) code. Phantom measurements showed a good accuracy of the technique and in vivo T(1) estimation of liver, skeletal muscle, myocardium, and blood resulted in good agreement with values reported in the literature. Multiple three-dimensional inversion recovery technique is a feasible and accurate method to perform T(1) volume mapping.

Validation of the new AJCC TNM staging system for gastric cancer in a large cohort of patients (n = 2,155): focus on the T category.

BACKGROUND: The prognostic value of T subclassification in patients with gastric carcinoma has been just implemented in the new AJCC TNM staging system, which has reclassified T2a and T2b into T2 and T3 tumors, respectively. The aim of the present study was to validate the prognostic significance of the new T categorization within the frame of the latest TNM staging system. METHODS: We retrospectively reviewed the records of 686 T2/T3 patients among 2155 subjects who underwent radical resection for gastric carcinoma at six Italian centers from 1988 through 2006. RESULTS: Upon multivariate analysis, the new T categories, extent of lymph node dissection (D) and patient's age were retained by the survival model as independent prognostic factors. In particular, the death risk for patients with T3 tumors was higher than that of patients with T2 tumors (HR: 1.42, P = 0.005). Among the 686 patients previously classified as having T2 tumors, patients with T2 and T3 disease were 270 (39.4%) and 416 (60.6%), respectively. After a median follow-up of 55 months, the 5-year overall survival rates were 67.3% and 52.3% for patients with T2 and T3 tumors, respectively (P < 0.001). The survival advantage for the T2 as compared to T3 category was maintained even when N0 and N+ patients were separately considered (P = 0.0154 and P < 0.001, respectively). CONCLUSIONS: Our data confirm the prognostic difference between the newly proposed T2 and T3 categories, which should be implemented in the routine clinical practice to improve risk stratification of patients with gastric cancer.

Changing clinical and pathological features of gastric cancer over time.

BACKGROUND: The aim of the present multicentre observational study was to evaluate potential changes in clinical and pathological features of patients with gastric cancer (GC) treated in a 15-year interval. METHODS: A centralized prospective database including clinical, surgical, pathological and follow-up data from 2822 patients who had resection of a primary GC was analysed. The analysis focused on three periods: 1991-1995 (period 1), 1996-2000 (period 2) and 2001-2005 (period 3). Surgical procedure, pathological classification and follow-up were standardized among centres. RESULTS: The number of resections decreased from 1024 in period 1 to 955 and 843 in periods 2 and 3 respectively. More advanced stages and a smaller number of intestinal-type tumours of the distal third were observed over time. Five-year survival rates after R0 resection (2320 patients) did not change over time (overall: 56·6 and 51·2 per cent in periods 1 and 3; disease-free: 66·8 and 61·1 per cent respectively). Decreases in survival in more recent years were related particularly to more advanced stage, distal tumours and tumours in women. Multivariable analysis showed a lower probability of overall and disease-free survival in the most recent interval: hazard ratio 1·22 (95 per cent confidence interval 1·06 to 1·40) and 1·29 (1·06 to 1·58) respectively compared with period 1. Recurrent tumours were more frequently peritoneal rather than locoregional. CONCLUSION: Overall and disease-free survival rates after R0 resection of GC were unchanged over time.

Emergence of complex behavior in gelling systems starting from simple behavior of single clusters.

A theoretical and numerically study of dynamical properties in the sol-gel transition is presented. In particular, the complex phenomenology observed experimentally and numerically in gelling systems is reproduced in the framework of percolation theory, under simple assumptions on the relaxation of single clusters. By neglecting the correlation between particles belonging to different clusters, the quantities of interest (such as the self intermediate scattering function, the dynamical susceptibility, the Van-Hove function, and the non-Gaussian parameter) are written as superposition of those due to single clusters. Connection between these behaviors and the critical exponents of percolation are given. The theoretical predictions are checked in a model for permanent gels, where bonds between monomers are described by a finitely extendable nonlinear elastic potential. The data obtained in the numerical simulations are in good agreement with the analytical predictions.

Self-tuning phase separation in a model with competing interactions inspired by biological cell polarization.

We present a theoretical study of a system with competing short-range ferromagnetic attraction and a long-range antiferromagnetic repulsion, in the presence of a uniform external magnetic field. The interplay between these interactions, at sufficiently low temperature, leads to the self-tuning of the magnetization to a value which triggers phase coexistence, even in the presence of the external field. The investigation of this phenomenon is performed using a Ginzburg-Landau functional in the limit of an infinite number of order parameter components (large N model). The scalar version of the model is expected to describe the phase separation taking place on a cell surface when this is immersed in a uniform concentration of chemical stimulant. A phase diagram is obtained as a function of the external field and the intensity of the long-range repulsion. The time evolution of the order parameter and of the structure factor in a relaxation process is studied in different regions of the phase diagram.

Metachronous hepatic metastases from gastric carcinoma: a multicentric survey.

BACKGROUND: The treatment of hepatic metastases from gastric cancer is controversial, due to biologic aggressiveness of the disease. OBJECTIVE: To survey the clinical approach to the subset of patients presenting with metachronous hepatic metastases as sole site of recurrence after curative resection of gastric cancer, focusing on the results achieved by different therapies and to investigate the prognostic factors of major clinical relevance. METHODS: Retrospective multi-center chart review evaluating 73 patients, previously submitted to D >or= 2 gastrectomy for gastric cancer, who developed exclusive hepatic recurrence. Prognostic factors related to the patient, to the gastric malignancy and its treatment, and to the metastatic disease and its therapy were evaluated. RESULTS: Forty-five patients received supportive care, 17 were submitted to chemotherapy, and 11 to hepatic resection. Survival was independently influenced by the variables T (p=0.019), N (p=0.05) and G (p=0.018) of the gastric primary and by the therapeutic approach to the metastases (p<0.005). In particular, T4 gastric cancer, presence of lymph-node metastases and G3 tumor displayed a negative prognostic value. Therapeutic approach to the metastases was the principal prognostic variable: 1, 2, and 3 years survival rates were 22.2%, 4.4% and 2.2%, respectively, for patients without specific treatment; 44.9%, 12.8% and 6.4% after chemotherapy (p=0.08) and 80.8%, 30.3% and 20.2% after surgical resection (p<0.001). CONCLUSIONS: Our data suggest some clinical criteria that may facilitate selection of therapy for patients with hepatic recurrence after primary gastric cancer resection. The best survival rates are associated with surgical treatment, which should be chosen whenever possible.

Dynamical heterogeneities in irreversible gels: analogy with spin glasses.

We describe the sol-gel transition by introducing an order parameter, defined as the average of local variables, and its fluctuations. It can be shown that these quantities are related to percolation quantities, but in principle they can be measured without resorting to connectivity properties. In this framework it appears that the dynamical transition associated with gelation is a real thermodynamic transition, as happens in spin glasses. The strong analogies between the sol-gel transition and the spin glass transition are also discussed.

Dynamical heterogeneity in a model for permanent gels: different behavior of dynamical susceptibilities.

We present a systematic study of dynamical heterogeneity in a model for permanent gels upon approaching the gelation threshold. We find that the fluctuations of the self-intermediate scattering function are increasing functions of time, reaching a plateau whose value, at large length scales, coincides with the mean cluster size and diverges at the percolation threshold. Another measure of dynamical heterogeneities-i.e., the fluctuations of the self-overlap-displays instead a peak and decays to zero at long times. The peak, however, also scales as the mean cluster size. Arguments are given for this difference in the long-time behavior. We also find that the non-Gaussian parameter reaches a plateau in the long-time limit. The value of the plateau of the non-Gaussian parameter, which is connected to the fluctuations of diffusivity of clusters, increases with the volume fraction and remains finite at the percolation threshold.

The prognostic value of N-ratio in patients with gastric cancer: validation in a large, multicenter series.

AIMS: The proportion between metastatic and examined lymph nodes (N-ratio) has been proposed as an independent prognostic factor in patients with gastric cancer. In the present work we validated the reliability of N-ratio in a large, multicenter series. PATIENTS AND METHODS: We retrospectively reviewed the data of 1853 patients who underwent radical resection for gastric carcinoma. Survival of patients with >15 (Group-1, n=1421) and those with < or =15 (Group-2, n=432) lymph nodes examined was separately analyzed in order to evaluate the influence of lymph node dissection on disease staging. N-ratio categories (N-ratio 0, 0%; N-ratio 1, 1-9%; N-ratio 2, 10-25%; N-ratio 3, >25%) were determined by the best cut-off approach. RESULTS: At multivariate analysis, N-ratio (but not TNM N-category) was retained as an independent prognostic factor both in Group-1 and Group-2 (HR for N-ratio 1, N-ratio 2 and N-ratio 3=1.67, 2.96 and 6.59, and 1.56, 2.68 and 4.28, respectively). After a median follow-up of 45.5 months, the 5-year overall survival rates of TNM N0, N1 and N2 patients were significantly different in Group-1 vs Group-2. This was not the case when adopting the N-ratio classification, suggesting that a low number of excised lymph nodes can lead to patients being understaged using the N-category, but not N-ratio. Moreover, N-ratio identified subsets of patients with significantly different survival rates within TNM N1 and N2 categories in both groups. CONCLUSIONS: N-ratio is a simple and reproducible prognostic tool that can stratify patients with gastric cancer, including those cases with limited lymph node dissection. These data support the rationale to propose the implementation of N-ratio into the current TNM staging system.

Static and dynamic heterogeneities in a model for irreversible gelation.

We study the structure and the dynamics in the formation of irreversible gels by means of molecular dynamics simulation of a model system where the gelation transition is due to the random percolation of permanent bonds between neighboring particles. We analyze the heterogeneities of the dynamics in terms of the fluctuations of the self-intermediate scattering functions: in the sol phase close to the percolation threshold, we find that this dynamic susceptibility increases with the time until it reaches a plateau. At the gelation threshold this plateau scales as a function of the wave vector k as k(eta-2), with eta being related to the decay of the percolation pair connectedness function. At the lowest wave vector, approaching the gelation threshold it diverges with the same exponent gamma as the mean cluster size. These findings suggest an alternative way of measuring critical exponents in a system undergoing chemical gelation.

Phenomenology and theory of horizontally oscillated granular mixtures.

We overview the physics of a granular mixture subject to horizontal oscillations, recently investigated via experiments and molecular dynamics simulations. First we discuss the rich phenomenology exhibited by this system, which encompasses both segregation and dynamical instabilities. Then we show that the phenomenology can be explained via an effective interaction approach, by which the driven, non-thermal, granular mixture in mapped into a monodispersed thermal system of particles interacting via an effective potential. After determining the effective interaction we discuss its microscopic origin and investigate how it induces the observed phenomenology. Finally, as much as in thermal fluids, from the effective interaction we derive a Cahn-Hilliard dynamics equation, which appears to capture the essential characteristics of the dynamics of the granular mixture.

Shear- and vibration-induced order-disorder transitions in granular media.

By molecular dynamics simulations we investigate the order-disorder transitions induced in granular media by an applied drive combining vibrations and shear. As the steady state is attained, the pack is found in disordered configurations for comparatively high intensities of the drive; conversely, ordering and packing fractions exceeding the random close packing are found when vibrations and shear are weak. As forcing amplitudes get smaller, we find diverging time scales in the dynamics, as the system enters a jamming region. Under this perspective, our picture supports the intuition that externally applied forcing has, in driven granular media, a role similar to temperature in thermal systems.