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Surface motility and biofilm formation are behaviours which enable bacteria to infect their hosts and are controlled by different chemical signals. In the plant symbiotic alpha-proteobacterium Sinorhizobium meliloti, the lack of long-chain fatty acyl-coenzyme A synthetase activity (FadD) leads to increased surface motility, defects in biofilm development and impaired root colonization. In this study, analyses of lipid extracts and volatiles revealed that a fadD mutant accumulates 2-tridecanone (2-TDC), a methylketone (MK) known as a natural insecticide. Application of pure 2-TDC to the wild-type strain phenocopies the free-living and symbiotic behaviours of the fadD mutant. Structural features of the MK determine its ability to promote S. meliloti surface translocation, which is mainly mediated by a flagella-independent motility. Transcriptomic analyses showed that 2-TDC induces differential expression of iron uptake, redox and stress-related genes. Interestingly, this MK also influences surface motility and impairs biofilm formation in plant and animal pathogenic bacteria. Moreover, 2-TDC not only hampers alfalfa nodulation but also the development of tomato bacterial speck disease. This work assigns a new role to 2-TDC as an infochemical that affects important bacterial traits and hampers plant-bacteria interactions by interfering with microbial colonization of plant tissues.

Data compiled during three fieldwork seasons and habitat models provided the tools to produce Species recovery plans for the endangered and endemic butterflies in Spain: Polyommatus violetae, P. golgus, Agriades zullichi, and Euchloe bazae. The distribution of each species has been updated with new field records. For E. bazae and P. violetae the known distribution records increased 33% and 8%, respectively. Detailed habitat descriptions, based on fieldwork data, are given for the four species and models show relatively small and fragmented habitat patches for P. violetae, P. golgus, and P. zullichi. Those areas might be particularly sensitive under a climate change scenario. Habitat of the four species is very specialized and mainly consists of open areas with grassland or scrub vegetation. Population densities are provided for the first time for these species and show low numbers for E. bazae, particularly in the area around Baza in SE Spain. 25 to 54% of the populations were apparently not threatened. For the rest, apparent habitat suitability threats were abandonment for E. bazae and P. violetae, trampling for A. zullichi, and overgrazing for P. golgus. Recovery plans included aspects on legislation, habitat management, precautionary measures (limit new developments and land use changes), research, and public awareness campaigns. Suggested habitat management actions are: (1) support extensive grazing and prevent overgrazing; (2) reduce the effect of trampling by visitors in mountain areas; and (3) woodland and scrub clearing of abandoned areas and pine plantations to improve the quality of grassland habitats.

The present investigation was aimed to evaluate the effect of varied amount of earthworm meal (EW) and vermihumus (VH) on the growth performance of broiler chickens. Three hundred 1-d-old broiler chickens were assigned to 5 starter treatments with 5 pens per treatment, and 12 broiler chickens per pen in a completely randomized design from d 0–14 of the study. Dietary treatments were [per kilogram dry matter (DM)]: control (0 g EW and 0 g VH/kg of DM), and the diets containing 10 g VH/kg of DM supplemented with 0, 10, 20, or 30 g EW/kg of DM. At the end of the study (d 42), one representative broiler chicken per pen, close to the average body weight, was selected for blood sampling using a sterile needle and heparinized vacuum tube. The outcomes of the study depicted the greater overall feed intake value in broiler chicken fed the control diet than those fed the diets containing VH or EW or both, and it decreased linearly and quadratically (P < 0.05) as the amount of EW supplementation increased. The average weight gain for the chickens was numerically increased as supplementation of EW was increased (linear, =0.3; quadratic P=0.4). On the other hand, overall feed conversation ratio was slightly greater (P=0.02) in broiler chickens fed the control diet, and it decreased linearly (P=0.03) as dietary EW supplementation increased. Additionally, the serum total protein, albumin, Ca, and P concentrations were lower in broiler chickens fed the control diet, and those variables increased linearly (P < 0.05) as dietary EW increased. In like manner, humoral immune response (except heterophil/lymphocyte ratio) and relative weights of immune organs were lower in broiler chickens fed the control diet. Remarkable differences were observed between carcass and ileum characteristics of broiler chickens under treatments. Varied concentrations of EW showed increased total counts of lactic acid bacteria (linear, P < 0.05; quadratic, P=0.3) and reduced population of pathogenic intestina

The present study aimed to investigate the effects of adding xylanase enzyme (XY) to a basal diet containing 300 g maize stover and 700 g concentrate/kg dry matter (DM) on feed intake, ruminal fermentation, total tract and ruminal digestibility, as well as some blood parameters. Four male Rambouillet sheep (39 ± 1·8 kg body weight), with permanent rumen and duodenum cannulae were used in a 4 × 4 Latin square design. Sheep were fed a basal diet without xylanase addition (control, XY0), or with the addition of xylanase at 1 (XY1), 3 (XY3) or 6 (XY6) ¿l/g of diet DM for 84 days, with four 21-day experimental periods. Feed intake, digestibility and rumen fermentation parameters were determined on days 16¿21 in each experimental period, and the apparent ruminal neutral detergent fibre (NDF) digestibility was determined on days 16 and 17. Treatments XY1 and XY3 increased feed intake, whereas digestibility was increased with XY6. Ruminal NDF digestibility increased when sheep were fed diets treated with xylanase. Ruminal pH, ammonia-N and acetic acid increased with xylanase treated diets. Propionic acid concentration increased with diet XY1 at 3 h post-feeding, but after 9 h post-feeding its concentration decreased in the rumen of sheep fed xylanase treated diets. Xylanase had no effect on blood urea, phosphorus and triglycerides. Addition of xylanase at 6 µl/g DM in a diet containing 300 g maize stover and 700 g concentrate/kg DM and fed to Rambouillet sheep improved feed digestibility and ruminal fermentation without affecting blood parameters.

[EN] The invention relates to a method for preventing and/or controlling bacterial infections in a plant and/or culture, and to products (raw food, washing solutions, material for use in hospitals) and facilities that are susceptible to contamination by bacteria, by means of the application of long-chain aliphatic methyl ketones, essentially 2-tridecanone but also 2-undecanone, 2-dodecanone, and 2-pentadecanone, in non-toxic forms and concentrations of a micromolar order such that they enable the prevention of said infection without producing a bactericide effect (destruction of bacteria). The invention also relates to said methyl ketones for use in medicine, by means of the administration of said compound to an animal or a human being, [ES] La presente invención se refiere a un método para prevenir y/o controlar infecciones bacterianas en una planta y/o cultivo, así como en productos (alimentos crudos, soluciones de lavado, material de uso hospitalario) e instalaciones susceptibles de contaminación por bacterias, mediante aplicación de metilcetonas alifáticas de cadena larga, fundamentalmente 2-tridecanona pero también 2-undecanona, 2- dodecanona, y 2-pentadecanona, en formas y concentraciones del orden micromolar no tóxicas tales que permiten evitar dicha infección sin producir un efecto bactericida (destrucción de bacterias). Asimismo, la presente invención se refiere a estas metilcetonas citadas para uso en medicina, mediante administración de dicho compuesto a un animal o un ser humano

La presente invención se refiere a un método para prevenir y/o controlar infecciones bacterianas en una planta y/o cultivo, así como en productos (alimentos crudos, soluciones de lavado, material de uso hospitalario) e instalaciones susceptibles de contaminación por bacterias, mediante aplicación de metilcetonas alifáticas de cadena larga, fundamentalmente 2-tridecanona pero también 2- undecanona, 2-dodecanona, y 2-pentadecanona, en formas y concentraciones del orden micromolar no tóxicas tales que permiten evitar dicha infección sin producir un efecto bactericida (destrucción de bacterias). Asimismo, la presente invención se refiere a estas metilcetonas citadas para uso en medicina, mediante administración de dicho compuesto a un animal o un ser humano

Optical properties of AgxAu1-x alloys were obtained experimentally using spectroscopic ellipsometry measurements on thin films fabricated by electron beam evaporation. Thin film thicknesses varied between 170 and 330 nm, making size effects negligible. Values of the complex refractive index of the pure metals were in good agreement with literature reports. The optical data set reported in this work can accurately reproduce experimental results. This is very important because there are not reliable and systematic optical constants for the alloys. Moreover, we show that the weighted average of the refractive indices of the pure metals fails to represent those of the alloys, not only in the region near the onset for interband transitions but also in the near-IR region. © 2014 Optical Society of America.

The implantation and irradiation beamline of the Tandem ion accelerator of the Centro de Micro Análisis de Materiales (CMAM), in Madrid, has been recently completed with a beam sweep and monitoring system, and a cryostat/furnace. These new implementations convert the beamline into a versatile tool to implant ions, between H and Au2, in different materials with precise control of the sample temperature, which may be varied between -180 °C and 600 °C. The size of the swept area on target may be as large as 10 × 10 cm2. The implantation chamber also allows carrying out in situ or/and on line analyses during the irradiations by means of advanced optical measurements, as well as ion beam analyses (IBA). These advancements can be employed in novel applications such as the fabrication of optical waveguides and irradiation tests of structural and functional materials for future fusion reactors. The results of beam tests and first experiments are shown. © 2014 Elsevier B.V. All rights reserved.

Deposits of exposed and embedded silver nanoparticles were grown on Si(100) and silica substrates by laser ablating high-purity silver and SiO2 targets in vacuum using a femtosecond Ti:sapphire laser delivering 45 fs pulses at 804 nm and 1 kHz repetition rate. The effect of the laser fluence and irradiation time on the obtained nanostructures was investigated using several fluences between 650 mJ/cm2 and 3.2 J/cm2 and deposition times in the range of 1-20 minutes. Optical response of the deposits was characterized using optical absorption spectroscopy and the surface morphology was studied by scanning electron microscopy (SEM). Samples with the optimal optical response were obtained by depositing three successive Ag/SiO2 bilayers at the main laser wavelength (804 nm) under vacuum at substrate room temperature. They were composed of silver nanoparticles with an average diameter of 6 nm and a narrow size distribution; each layer of these nanoparticles was then separated by silica layers of approximately 100 nm. The laser fluence and deposition time for Ag (SiO2) were 650 mJ/cm2 (3.2 J/cm2) and 1 min (10 min), respectively. © 2014 Optical Society of America.

We report on the successful trapping and patterning of micro- and nanometric particles on the surface of LiNbO3 optical waveguides via photovoltaic tweezers. A waveguide configuration is used for the first time combined with this recently proposed technique. The electric field pattern is generated by light propagating in the waveguide, allowing us to separate the light channel with the region in which particles are deposited. Results on microand nanoparticle trapping, by two different deposition methods on two types of planar waveguides (by soft proton exchanged and by swift heavy ion irradiation), and using single-beam and two-beam interferometric configuration, are presented and discussed. © 2014 Optical Society of America.

Ionoluminescence (IL) has been used in this work as a sensitive tool to probe the microscopic electronic processes and structural changes produced on quartz by the irradiation with swift heavy ions. The IL yields have been measured as a function of irradiation fluence and electronic stopping power. The results are consistent with the assignment of the 2.7 eV (460 nm) band to the recombination of self-trapped excitons at the damaged regions in the irradiated material. Moreover, it was possible to determine the threshold for amorphization by a single ion impact, as ˜1.7 keV/nm, which agrees well with the results of previous studies. © 2012 The Japan Society of Applied Physics.

Systematic data on the effect of irradiation with swift ions (Zn at 735MeV and Xe at 929MeV) on NaCl single crystals have been analysed in terms of a synergetic two-spike approach (thermal and excitation spikes). The coupling of the two spikes, simultaneously generated by the irradiation, contributes to the operation of a non-radiative exciton decay model as proposed for purely ionization damage. Using this scheme, we have accounted for the -emission yield of self-trapped excitons and its temperature dependence under ion-beam irradiation. Moreover, the initial production rates of F-centre growth have also been reasonably simulated for irradiation at low temperatures (<100K), where colour centre annealing and aggregation can be neglected. © 2012 IOP Publishing Ltd.

The refractive index changes induced by swift ion-beam irradiation in silica have been measured either by spectroscopic ellipsometry or through the effective indices of the optical modes propagating through the irradiated structure. The optical response has been analyzed by considering an effective homogeneous medium to simulate the nanostructured irradiated system consisting of cylindrical tracks, associated to the ion impacts, embedded into a virgin material. The role of both, irradiation fluence and stopping power, has been investigated. Above a certain electronic stopping power threshold (∼2.5 keV/nm), every ion impact creates an axial region around the trajectory with a fixed refractive index (around n = 1.475) corresponding to a certain structural phase that is independent of stopping power. The results have been compared with previous data measured by means of infrared spectroscopy and small-angle X-ray scattering; possible mechanisms and theoretical models are discussed. © 2012 Elsevier B.V. All rights reserved.

The photorefractive effect and the corresponding optical damage thresholds of novel LiNbO 3 waveguides fabricated by swift ion irradiation have been investigated. TE- and TM-mode operation have been characterized, and the influence of the beam propagation length analyzed. Optical damage levels similar to those of proton-exchanged waveguides have been found. In order to reduce optical damage, the influence of temperature has been investigated. An increase of more than a factor of 100 in the optical damage threshold has been obtained by moderate heating up to 90°C. The results are briefly discussed under the two-center model for the photorefractive effect in undoped LiNbO 3, and compared with data from other types of LiNbO 3 waveguides. © 2012 Optical Society of America.

A simple illustrative physical model is presented to describe the kinetics of damage and amorphization by swift heavy ions (SHI) in LiNbO3. The model considers that every ion impact generates initially a defective region (halo) and a full amorphous core whose relative size depends on the electronic stopping power. Below a given stopping power threshold only a halo is generated. For increasing fluences the amorphized area grows monotonically via overlapping of a fixed number N of halos. In spite of its simplicity the model, which provides analytical solutions, describes many relevant features of the kinetic behaviour. In particular, it predicts approximate Avrami curves with parameters depending on stopping power in qualitative accordance with experiment that turn into Poisson laws well above the threshold value. © 2010 Elsevier B.V. All rights reserved.

Plant-interacting bacteria can establish either mutualistic or pathogenic interactions that cause beneficial or detrimental effects respectively, to their hosts. In spite of the completely different outcomes, accumulating evidence indicates that similar molecular bases underlie the establishment of these two contrasting plant-bacteria associations. Recent findings observed in the mutualistic nitrogen-fixing Rhizobium-legume symbiosis add new elements to the increasing list of similarities. Amongst these, in this review we describe the role of plant resistance proteins in determining host specificity in the Rhizobium-legume symbiosis that resemble the gene-for-gene resistance of plant-pathogen interactions, and the production of antimicrobial peptides by certain legumes to control rhizobial proliferation within nodules. Amongst common bacterial strategies, cyclic diguanylate (c-di-GMP) appears to be a second messenger used by both pathogenic and mutualistic bacteria to regulate key features for interaction with their plant hosts.

The elastic strain/stress fields (halo) around a compressed amorphous nano-track (core) caused by a single high-energy ion impact on LiNbO3 are calculated. A method is developed to approximately account for the effects of crystal anisotropy of LiNbO3 (symmetry 3m) on the stress fields for tracks oriented along the crystal axes (X, Y or Z). It only considers the zero-order (axial) harmonic contribution to the displacement field in the perpendicular plane and uses effective Poisson moduli for each particular orientation. The anisotropy is relatively small; however, it accounts for some differential features obtained for irradiations along the crystallographic axes X, Y and Z. In particular, the irradiation-induced disorder (including halo) and the associated surface swelling appear to be higher for irradiations along the X- or Y-axis in comparison with those along the Z-axis. Other irradiation effects can be explained by the model, e.g. fracture patterns or the morphology of pores after chemical etching of tracks. Moreover, it offers interesting predictions on the effect of irradiation on lattice parameters. © 2011 IOP Publishing Ltd.

The thermal annealing of amorphous tracks of nanometer-size diameter generated in lithium niobate (LiNbO3) by Bromine ions at 45 MeV, i.e., in the electronic stopping regime, has been investigated by RBS/C spectrometry in the temperature range from 250°C to 350°C. Relatively low fluences have been used (<1012 cm-2) to produce isolated tracks. However, the possible effect of track overlapping has been investigated by varying the fluence between 3×1011 cm -2and 1012 cm-2. The annealing process follows a two-step kinetics. In a first stage (I) the track radius decreases linearly with the annealing time. It obeys an Arrhenius-type dependence on annealing temperature with activation energy around 1.5 eV. The second stage (II) operates after the track radius has decreased down to around 2.5 nm and shows a much lower radial velocity. The data for stage I appear consistent with a solid-phase epitaxial process that yields a constant recrystallization rate at the amorphouscrystalline boundary. HRTEM has been used to monitor the existence and the size of the annealed isolated tracks in the second stage. On the other hand, the thermal annealing of homogeneous (buried) amorphous layers has been investigated within the same temperature range, on samples irradiated with Fluorine at 20 MeV and fluences of ∼1014 cm-2. Optical techniques are very suitable for this case and have been used to monitor the recrystallization of the layers. The annealing process induces a displacement of the crystallineamorphous boundary that is also linear with annealing time, and the recrystallization rates are consistent with those measured for tracks. The comparison of these data with those previously obtained for the heavily damaged (amorphous) layers produced by elastic nuclear collisions is summarily discussed. © Springer-Verlag 2011.

The non-radiative exciton decay model recently developed to account for swift-ion-beam damage to LiNbO3 is, here, discussed within a general physical perspective, taking previous work on alkali halides as a reference. Some general rules for the validity of excitonic models have been put forward, allowing one to predict the irradiation behaviour of other materials. As a new example of application, some preliminary data on the generation and growth of uniform amorphous layers induced by irradiation with Br at 13 MeV and 25 MeV have been performed on rutile (TiO2). In addition sub-threshold irradiations with Br ions at 9 MeV have been carried out. Defects generation is observed as a result. This effect is explained with the exciton model. Experiments are in the electronic excitation regime and use moderate fluences in the range of 6 × 1012 to 1.5 × 1014 cm−2. The results show similar features to those found for LiNbO3 and are, in principle, consistent with a non-radiative exciton decay model. © 2010 Elsevier B.V. All rights reserved

The preparation of optical waveguides for visible light in silica (a-SiO2) by means of swift heavy-ion irradiation (F at 5 MeV, Cl at 20 MeV) is reported. They originate from the refractive index enhancement (compaction) brought about by the electronic excitation. Their main features are discussed in relation to those prepared by light ion irradiation (H, He) and implantation. In particular, irradiation fluences to achieve waveguiding may be considerably reduced. On the other hand, the measured refractive index profiles have been used to discuss the mechanisms of electronic damage. Moreover, the measurement of the index profiles provides a novel optical method, alternative to IR spectroscopy, to estimate the radius of the irradiation-induced tracks. © 2010 Elsevier B.V. All rights reserved.

We present a MonteCarlo approach to the non-radiative exciton-decay model recently proposed to describe ion-beam damage in LiNbO3 produced in the electronic excitation regime. It takes into account the statistical (random) spatial distribution of ion impacts on the crystal surface. The MonteCarlo approach is necessary to simulate the evolution of the damage morphology with irradiation fluence from the single track regime to the overlapping track regime. A detailed comparison between the morphologies found for sub-threshold and above threshold irradiations is presented. Moreover, a good representation of the Avrami’s type kinetics for amorphization has been achieved and it is in fair accordance with experiment. For moderate fluences where homogeneous amorphous layers are generated, the new approach predicts that the amorphous and crystalline layers are separated by a diffuse (thick) boundary that includes a mixed amorphous-crystalline composition.

[Background] Swarming is a multicellular phenomenom characterized by the coordinated and rapid movement of bacteria across semisolid surfaces. In Sinorhizobium meliloti this type of motility has been described in a fadD mutant. To gain insights into the mechanisms underlying the process of swarming in rhizobia, we compared the transcriptome of a S. meliloti fadD mutant grown under swarming inducing conditions (semisolid medium) to those of cells grown under non-swarming conditions (broth and solid medium)., [Results] More than a thousand genes were identified as differentially expressed in response to growth on agar surfaces including genes for several metabolic activities, iron uptake, chemotaxis, motility and stress-related genes. Under swarming-specific conditions, the most remarkable response was the up-regulation of iron-related genes. We demonstrate that the pSymA plasmid and specifically genes required for the biosynthesis of the siderophore rhizobactin 1021 are essential for swarming of a S. meliloti wild-type strain but not in a fadD mutant. Moreover, high iron conditions inhibit swarming of the wild-type strain but not in mutants lacking either the iron limitation response regulator RirA or FadD., [Conclusions] The present work represents the first transcriptomic study of rhizobium growth on surfaces including swarming inducing conditions. The results have revealed major changes in the physiology of S. meliloti cells grown on a surface relative to liquid cultures. Moreover, analysis of genes responding to swarming inducing conditions led to the demonstration that iron and genes involved in rhizobactin 1021 synthesis play a role in the surface motility shown by S. meliloti which can be circumvented in a fadD mutant. This work opens a way to the identification of new traits and regulatory networks involved in swarming by rhizobia.

The surface morphology of the ablation craters generated in LiNbO3 by 130 fs laser pulses at 800 nm has been investigated by AFM/SNOM microscopy. The single pulse fluence corresponding to the ablation threshold has been estimated to be ≈1.8 J/cm2. A complex structure including random cone-shaped protrusions is observed inside the ablated crater. The scale of the protrusion spacing is in the submicron range and the heights are typically of a few tens of nanometers. At and outside the crater rim a novel quasi-periodic wave-like topography pattern is observed in both types of microscopy techniques. The average wavelength, that is slightly dependent on pulse fluence, is (500-800 nm) comparable to the light wavelength. This novel topography feature keeps a close similarity with a Fresnel diffraction pattern by an absorbing circular obstacle or impact wave pattern produced by a combination of heat and shock wave (resemble that of impact crater). It is proposed that the obstacle is associated to the strongly nonlinear multiphoton absorption at the peak of the pulse profile. The energy deposited by nonlinear absorption of such profile causes ablation of both the crater and the rippled structure. © 2008.

We report on the characterization of planar waveguides formed in the Raman-active crystal KGd(WO4)2 using swift carbon, fluorine, and oxygen ion irradiation. The characterization of the waveguiding regions was performed using high-resolution microreflectivity and micro-Raman spectroscopy. The high-resolution microreflectivity measurement fully characterizes the refractive index profile of the barrier formed by amorphization of the crystal and detects other index variations not detected by the m-line technique. Raman spectroscopy measurements reveal details of the Raman properties of the crystal in the waveguiding region in relation to the rest of the sample for the different ion irradiations. Both of these measurement techniques are shown to be important for use of KGd(WO4)2 in integrated Raman-active devices. © 2009 IEEE.

Periodically poled swift-ion irradiated waveguides have been prepared following two different methods: i) Ion irradiation of two types of periodically poled lithium niobate (PPLN), that is, Czochralski off-centred grown PPLN and external electrical field PPLN. After the ion irradiation, the domain structure of the original PPLN was preserved and the waveguides were also proved functional. ii) Electric periodical poling of previously fabricated swift-ion irradiated waveguides. The periodic polarization of the ion irradiated waveguide was achieved for the first time to our knowledge. In both cases, the combination of PPLN with optical waveguide structures created by swift-ion irradiation, which have good nonlinear and electrooptical properties, and high optical confinement, gives rise to quite good candidates for nonlinear optical devices. © Taylor & Francis 2009

The morphology of the nanopores obtained by chemical etching on ion-beam irradiated LiNbO3 has been investigated for a variety of ions (F, Br, Kr, Cu, Pb), energies (up to 2300 MeV), and stopping powers (up to 35 keV/nm) in the electronic energy loss regime. The role of etching time and etching agent on the pore morphology, diameter, depth, and shape has also been studied. The transversal and depth profiles of the pore have been found to be quite sensitive to both irradiation and etching parameters. Moreover, two etching regimes with different morphologies and etching rates have been identified. © 2009.

A theoretical strategy is developed to quantitatively assess the ion-beam damage as measured by Rutherford-backscattering spectrometry under channeling conditions (RBS/C) in LiNbO3 crystals. The approach is based on a recent exciton decay model to calculate the concentration of defects generated by the incoming ions as a function of their stopping power. To describe the channeled RBS yield the model takes into account the amorphous (core) as well as the defective halo contributions to the defect tracks caused by the ion impacts. It is concluded that the halo may significantly influence the assessed damage. © 2009 Elsevier B.V. All rights reserved.

The photorefractive behaviour of a novel type of optical waveguides fabricated in LiNbO3 by swift heavy ion irradiation is investigated. First, the electro-optic coefficient r 33 of these guides that is crucial in the photorefractive effect is measured. Second, two complementary aspects of the photorefractive response are studied: (i) recording and light-induced and dark erasure of holographic gratings; (ii) optical beam degradation in single-beam configuration. The main photorefractive parameters, recording and erasing time constants, maximum refractive-index change and optical damage thresholds are determined. © 2009 Springer-Verlag.

[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 of nodulation genes. Moreover, the Nod factor precursor, N-acetyl glucosamine reduces nod gene expression and nodulation efficiency when present at millimolar concentrations. A role for Tep1 in the efflux of Nod factor precursors could explain the phenotypes associated with tep1 inactivation.

(N-rich) Cu3N polycrystalline films were deposited by DC triode sputtering from a copper target in a mixture of argon and nitrogen atmosphere. Their chemical composition, structure and electrical properties have been studied as a function of deposition parameters: nitrogen partial pressure (PN2) and DC bias. Depending on PN2 and DC bias, the atomic nitrogen incorporated into the layers ranges from 26 at% to a limit value of 33 at% as measured by ion beam analysis (IBA) techniques. X-ray diffraction (XRD) data show that most of the layers are single phase, polycrystalline and with preferential 1 0 0 orientation. Optical and electrical measurements indicate that all layers present intrinsic semiconductor behavior with a thermal gap around 0.21–0.25 eV and a direct optical gap between 1.5 and 1.7 eV. The physical properties observed for these films are discussed in relation to nitrogen contents and sputtering parameters.

The lattice disorder generated in LiNbO3 by electronic excitation is quantitatively assessed and compared to that produced by elastic nuclear collisions. In particular, the main differential features between the two mechanisms are clearly established. The analysis is based on a recent non-radiative exciton decay model. For ions with atomic mass ≥15, the local damage caused by electronic excitation is strongly enhanced (up to three orders of magnitude) in comparison to that predicted by nuclear collisions. © 2008 Elsevier B.V. All rights reserved.

Relevant damage features associated with femtosecond pulse laser and swift-ion irradiations on LiNbO3 crystals are comparatively discussed. Experiments described in this paper include irradiations with repetitive femtosecond-laser pulses (800 nm, 130 fs) and irradiation with O, F, Si, and Cl ions at energies in the range of 0.2-1 MeV/amu where electronic stopping power is dominant. Data are semiquantitatively discussed by using a two-step phenomenological scheme. The first step corresponds to massive electronic excitation either by photons (primarily three-photon absorption) or ions (via ion-electron collisions) leading to a dense electron-hole plasma. The second step involves the relaxation of the stored excitation energy causing bond breaking and defect generation. It is described at a phenomenological level within a unified thermal spike scheme previously developed to account for damage by swift ions. A key common feature for the two irradiation sources is a well-defined intrinsic threshold in the deposited energy density Uth required to initiate observable damage in a pristine crystal: Uth ≈1.3× 104 -2× 104 J/ cm3 for amorphization in the case of ions and Uth ≈7× 104 J/ cm3 for ablation in the case of laser pulses. The morphology of the heavily damaged regions (ion-induced tracks and laser-induced craters) generated above threshold and its evolution with the deposited energy are also comparatively discussed. The data show that damage in both types of experiments is cumulative and increases on successive irradiations. As a consequence, a certain incubation energy density has to be delivered either by the ions or laser photons in order to start observable damage under subthreshold conditions. The parallelism between the effects of laser pulses and ion impacts is well appreciated when they are described in terms of the ratio between the deposited energy density and the corresponding threshold value. © 2008 American Institute of Physics.

The formation of buried heavily damaged and amorphous layers by a variety of swift-ion irradiations (F at 22 MeV, O at 20 MeV, and Mg at 28 MeV) on congruent LiNb O3 has been investigated. These irradiations assure that the electronic stopping power Se (z) is dominant over the nuclear stopping Sn (z) and reaches a maximum value inside the crystal. The structural profile of the irradiated layers has been characterized in detail by a variety of spectroscopic techniques including dark-mode propagation, micro-Raman scattering, second-harmonic generation, and Rutherford backscattering spectroscopychanneling. The growth of the damage on increasing irradiation fluence presents two differentiated stages with an abrupt structural transition between them. The heavily damaged layer reached as a final stage is optically isotropic (refractive index n=2.10, independent of bombarding ion) and has an amorphous structure. Moreover, it has sharp profiles and its thickness progressively increases with irradiation fluence. The dynamics under irradiation of the amorphous-crystalline boundaries has been associated with a reduction of the effective amorphization threshold due to the defects created by prior irradiation (cumulative damage). The kinetics of the two boundaries of the buried layer is quite different, suggesting that other mechanisms aside from the electronic stopping power should play a role on ion-beam damage. © 2007 American Institute of Physics.

A novel method to produce optical waveguides is demonstrated for lithium niobate (LiNbO3). It is based on electronic excitation damage by swift ions, i.e., with energies at approximately 1 MeV/amu or above. The new technique uses high-energy medium-mass ions, such as Cl, with electronic stopping powers above the threshold value for amorphization (5-6 keV/nm), reaching the maximum value a few micrometers inside the crystal. At the ultralow fluence regime (1012-1013 cm-2) an effective nanostructured medium is obtained that behaves as an optical waveguide where light propagates transversally to the amorphous nanotracks created by every single impact. The method implies a reduction of 4 orders of magnitude with respect to He implantation. The optical waveguides present reasonable losses (∼10 dB/cm) and significant second-harmonic generation (SHG) and electro-optic (EO) responses (>50% bulk) for the lowest fluences. © 2007 Optical Society of America.

A general theoretical framework to describe crystal damage and amorphization under swift-ion-beam irradiation is discussed. Main physical channels accounting for electron energy losses are considered: (a) phonon generation (heating) and (b) exciton localization and de-excitation. Two alternative schemes are analyzed. In one of them, intrinsic defects are generated through a direct thermal process, i.e. through channel (a). Above a certain threshold rate of electronic energy deposition the temperature reaches the melting point and the crystal becomes amorphous. In the other scheme, defects are generated through non-radiative de-excitation of excitons, formed during the final stage of electron slowing down. This may require to overcome a certain potential energy barrier. In this case the necessary thermal energy is provided by coupling to channel (a). The two schemes are discussed in the light of available experimental information. © 2006 Elsevier B.V. All rights reserved.

Irradiations with F, O at 25 MeV and C at 14 MeV energy have been performed in KGd(WO4)2 (KGW) in order to fabricate optical waveguides by a novel route based on ion irradiation instead of ion implantation. The method relies on selecting the energy high enough so as to place the maximum of the electronic stopping power a few microns inside the crystal. Then, buried isotropic layers (amorphous-like) are formed which have a low refractive index value of 1.87 (compared to the three crystalline values which are above 2.0). The refractive index profiles obtained are Gaussian-like with O ions and more step-like with the usage of C ions. Fairly low fluences in the range 1 × 1013-1 × 1014 have been successfully explored. The results have been compared to those recently obtained for LiNbO3 and have been analyzed with a theoretical model based on thermal spike concept. © 2006 Elsevier B.V. All rights reserved.

The surface of LiNbO3 crystals after swift ion irradiation in the low velocity regime has been investigated by optical and atomic force microscopy (AFM). Samples were irradiated with Cu 50 MeV, Cl 46 MeV and Br 12 MeV ions. Before any additional treatment the surface of the sample irradiated with Cu ions shows hillocks of a 5-8 nm diameter and of 5 nm in height. The latent tracks were subsequently etched at room temperature with HF:HNO3 solutions during a few minutes. The shape of the surface pore caused by etching was strongly anisotropic for the Cu irradiations and only slightly anisotropic for the Br irradiations. The larger track length and surface stopping power for the Cu 50 MeV ions is most likely the origin of the final difference in pore shape via the induced swelling and enhanced etching rate. Optical waveguide measurements were also performed in the case of Cl irradiations to obtain in-depth averaged values of internal amorphization and track radius. © 2006 Elsevier B.V. All rights reserved.

A theoretical model is proposed to account for the damage and amorphization induced in LiNbO3 by ion bombardment in the electronic energy-loss regime. It relies on the synergy between the thermal spike generated by electron-phonon interaction and the nonradiative decay of localized (self-trapped) excitons. Calculations have been carried out to describe the effect of single impact as well as multiple impact (high fluence) irradiations. In the first case, the defect concentration profile and the radius of the amorphous tracks have been theoretically predicted and they are in good accordance with those experimentally determined. For high fluence irradiations (1013 cm-2) the model predicts the formation of homogeneous amorphous surface layers whose thickness increases with fluence. The propagation of the crystalline-amorphous boundary has been determined as a function of irradiation fluence. Theoretical predictions are also in good agreement with experimental data on Si-irradiated (7.5 and 5 MeV) LiNbO3 outside the region of nuclear collision damage. © 2006 The American Physical Society.

Three-dimensional (3D) profiles of single nanotracks generated by a low impact density of Cl ions at 46 MeV have been determined by optical methods, using an effective-medium approach. The buried location of the maximum stopping power induces a surface optical waveguiding layer even at ultralow fluences (1011-1013 at./cm2) that allows to obtain the effective refractive index profiles (from dark-mode measurements). Combining the optical information with Rutherford backscattering spectroscopy/channeling experiments, the existence of a surrounding defective halo around the amorphous track core has been ascertained. The 3D profile of the halo has also been determined. © 2006 American Institute of Physics.

Genetic and biochemical characterization of TraA, the relaxase of symbiotic plasmid pRetCFN42d from Rhizobium etli, is described. After purifying the relaxase domain (N265TraA), we demonstrated nic binding and cleavage activity in vitro and thus characterized for the first time the nick site (nic) of a plasmid in the family Rhizobiaceae. We studied the range of N265TraA relaxase specificity in vitro by testing different oligonucleotides in binding and nicking assays. In addition, the ability of pRetCFN42d to mobilize different Rhizobiaceae plasmid origins of transfer (oriT) was examined. Data obtained with these approaches allowed us to establish functional and phylogenetic relationships between different plasmids of this family. Our results suggest novel characteristics of the R. etli pSym relaxase for previously described conjugative systems, with emphasis on the oriT cis-acting preference of this enzyme and its possible biological relevance.

A thermal-spike model has been applied to characterize the damage structure of the latent tracks generated by high-energy ion irradiations on LiNb O3 through electron excitation mechanisms. It applies to ions having electronic stopping powers both below and above the threshold value for lattice amorphization. The model allows to estimate the defect concentrations in the heavily damaged (preamorphized) regions that have not reached the threshold for amorphization. They include the halo and tail surrounding the core of a latent track. The existence of the preamorphized regions accounts for a synergy between successive irradiations and predicts a dependence of the amorphization threshold on previous irradiation fluence. The predicted dependence is in accordance with irradiation experiments using N (4.53 MeV), O (5.00 MeV), F (5.13 MeV), and Si (5 and 7.5 MeV). For electronic stopping powers above the threshold value the model describes the generation of homogeneous amorphous layers and predicts the propagation of the amorphization front with fluence. A theoretical expression, describing this propagation, has been obtained that is in reasonable agreement with silicon irradiation experiments at 5 and 7.5 MeV. The accordance is improved by including in a simple phenomenological way the velocity effect on the threshold. At the highest fluences (or depths) a significant discrepancy appears that may be attributed to the contribution of the nuclear collision damage. © 2005 American Institute of Physics.

The refractive-index profiles induced by high-energy (5 MeV, 7.5 MeV) silicon irradiation in LiNbO3 have been systematically determined as a function of ion fluence in the range 1013-1015 cm -2. At variance with irradiations at lower energies, an optically isotropic ('amorphous') homogeneous surface layer is generated whose thickness increases with fluence. These results have been associated with an electronic excitation mechanism. They are discussed in relation to the well-documented phenomenon of latent (amorphous) track generation under ion irradiation, requiring a threshold value Se,th for the electronic stopping power Se. Our optical data have yielded a value of ≈5 keV/nm for such a threshold, within the range reported by independent single-track measurements. The propagation of the amorphous boundary into the crystal during irradiation indicates that the threshold value decreases on increasing the fluence. Complementary Rutherford backscattering-channeling and micro-Raman (on samples irradiated at 30 MeV) experiments have been performed to monitor the induced structural changes. © Springer-Verlag 2005.

We analyze the limitations imposed by sample absorption on the determination of the nonlinear refractive index by the Z-scan technique. By using a nanostructured thin film consisting of Cu nanocrystals embedded in a dielectric Al2O3 matrix as an example, we show that thermo-optical effects appearing when linear absorption is significant can be strongly misleading in the interpretation of the results of a Z scan. Even though this effect is not new, the widespread use of the Z-scan technique during the past several years makes it necessary to analyze explicitly the conditions under which the technique can be reliably applied and when more sophisticated techniques should be used instead. We discuss the contributions to the signal under different experimental conditions, several diagnostic techniques to discriminate true nonlinear effects from thermally induced phenomena, and different methods to reduce the thermal contribution. © 2002 Optical Society of America.