The CBRB regulon: Promoter dissection reveals novel insights into the CbrAB expression network in Pseudomonas putida

CbrAB is a high ranked global regulatory system exclusive of the Pseudomonads that responds to carbon limiting conditions. It has become necessary to define the particular regulon of CbrB and discriminate it from the downstream cascades through other regulatory components. We have performed in vivo binding analysis of CbrB in P. putida and determined that it directly controls the expression of at least 61 genes; 20% involved in regulatory functions, including the previously identified CrcZ and CrcY small regulatory RNAs. The remaining are porines or transporters (20%), metabolic enzymes (16%), activities related to protein translation (5%) and orfs of uncharacterised function (38%). Amongst the later, we have selected the operon PP2810-13 to make an exhaustive analysis of the CbrB binding sequences, together with those of crcZ and crcY. We describe the implication of three independent non-palindromic subsites with a variable spacing in three different targets; CrcZ, CrcY and operon PP2810-13 in the CbrAB activation. CbrB is a quite peculiar σN—depen-dent activator since it is barely dependent on phosphorylation for transcriptional activation. With the depiction of the precise contacts of CbrB with the DNA, the analysis of the multi-merisation status and its dependence on other factors such as RpoN o IHF, we propose a model of transcriptional activation.Ministerio de Economía y Competitividad BIO2014-57545-

Weed discrimination using ultrasonic sensors

A new approach is described for automatic discrimination between grasses and broad-leaved weeds, based on their heights. An ultrasonic sensor was mounted on the front of a tractor, pointing vertically down in the inter-row area, with a control system georeferencing and registering the echoes reflected by the ground or by the various leaf layers. Static measurements were taken at locations with different densities of grasses (Sorghum halepense) and broad-leaved weeds (Xanthium strumarium and Datura spp.). The sensor readings permitted the discrimination of pure stands of grasses (up to 81% success) and pure stands of broad-leaved weeds (up to 99% success). Moreover, canonical discriminant analysis revealed that the ultrasonic data could separate three groups of assemblages: pure stands of broad-leaved weeds (lower height), pure stands of grasses (higher height) and mixed stands of broad-leaved and grass weeds (medium height). Dynamic measurements confirmed the potential of this system to detect weed infestations. This technique offers significant promise for the development of real-time spatially selective weed control techniques, either as the sole weed detection system or in combination with other detection tools.This research was funded by the Spanish CICyT (project AGL 2008-04670-C03)

In situ spectroellipsometric study of the nucleation and growth of amorphous silicon

A detailed in situ spectroellipsometric analysis of the nucleation and growth of hydrogenated amorphous silicon (a:Si:H) is presented. Photoelectronic quality a‐Si:H films are deposited by plasma‐enhanced chemical vapor deposition on smooth metal (NiCr alloy) and crystalline silicon (c‐Si) substrates. The deposition of a‐Si:H is analyzed from the first monolayer up to a final thickness of 1.2 μm. In order to perform an improved analysis, real time ellipsometric trajectories are recorded, using fixed preparation conditions, at various photon energies ranging from 2.2 to 3.6 eV. The advantage of using such a spectroscopic experimental procedure is underlined. New insights into the nucleation and growth mechanisms of a‐Si:H are obtained. The nucleation mechanism on metal and c‐Si substrates is very accurately described assuming a columnar microstructural development during the early stage of the growth. Then, as a consequence of the incomplete coalescence of the initial nuclei, a surface roughness at the 10-15 Å scale is identified during the further growth of a‐Si:H on both substrates. The bulk a‐Si:H grows homogeneously beneath the surface roughness. Finally, an increase of the surface roughness is evidenced during the long term growth of a‐Si:H. However, the nature of the substrate influenced the film growth. In particular, the film thickness involved in the nucleation‐coalescence phase is found lower in the case of c‐Si (67±8 Å) as compared to NiCr (118±22 Å). Likewise films deposited on c‐Si present a smaller surface roughness even if thick samples are considered (>1 μm). More generally, the present study illustrates the capability of in situ spectroellipsometry to precisely analyze fundamental processes in thin‐film growth, but also to monitor the preparation of complex structures on a few monolayers scale

Influence of pressure and radio frequency power on deposition rate and structural properties of hydrogenated amorphous silicon thin films prepared by plasma deposition

The influence of radio frequency (rf) power and pressure on deposition rate and structural properties of hydrogenated amorphous silicon (a-Si:H) thin films, prepared by rf glow discharge decomposition of silane, have been studied by phase modulated ellipsometry and Fourier transform infrared spectroscopy. It has been found two pressure regions separated by a threshold value around 20 Pa where the deposition rate increases suddenly. This behavior is more marked as rf power rises and reflects the transition between two rf discharges regimes. The best quality films have been obtained at low pressure and at low rf power but with deposition rates below 0.2 nm/s. In the high pressure region, the enhancement of deposition rate as rf power increases first gives rise to a reduction of film density and an increase of content of hydrogen bonded in polyhydride form because of plasma polymerization reactions. Further rise of rf power leads to a decrease of polyhydride bonding and the material density remains unchanged, thus allowing the growth of a-Si:H films at deposition rates above 1 nm/s without any important detriment of material quality. This overcoming of deposition rate limitation has been ascribed to the beneficial effects of ion bombardment on the a-Si:H growing surface by enhancing the surface mobility of adsorbed reactive species and by eliminating hydrogen bonded in polyhydride configurations

Potential of a terrestrial LiDAR-based system to characterise weed vegetation in maize crops

LiDAR (Light Detection And Ranging) is a remote-sensing technique for the measurement of the distance between the sensor and a target. A LiDAR-based detection procedure was tested for characterisation of the weed vegetation present in the inter-row area of a maize field. This procedure was based on the hypothesis that weed species with different heights can be precisely detected and discriminated using non-contact ranging sensors such as LiDAR. The sensor was placed in the front of an all-terrain vehicle, scanning downwards in a vertical plane, perpendicular to the ground, in order to detect the profile of the vegetation (crop and weeds) above the ground. Measurements were taken on a maize field on 3 m wide (0.45 m2) plots at the time of post-emergence herbicide treatments. Four replications were assessed for each of the four major weed species: Sorghum halepense, Cyperus rotundus, Datura ferox and Xanthium strumarium. The sensor readings were correlated with actual, manually determined, height values (r2 = 0.88). With canonical discriminant analysis the high capabilities of the system to discriminate tall weeds (S. halepense) from shorter ones were quantified. The classification table showed 77.7% of the original grouped cases (i.e., 4800 sampling units) correctly classified for S. halepense. These results indicate that LiDAR sensors are a promising tool for weed detection and discrimination, presenting significant advantages over other types of non-contact ranging sensors such as a higher sampling resolution and its ability to scan at high sampling rates.This research was funded by the Spanish CICyT (Project AGL 2008-04670-C03

Ultrafine particles produced by plasma enhanced chemical vapor deposition -from SiH4, CH4, NH3 and B2H6 gas mixtures- for nanostructured ceramics applications

[eng] Ultrafine particles of silicon and related binary and ternary alloys of the Si-B-C-N system produced in our research group from silane, methane, diborane, ammonia and nitrogen precursor gases by plasma enhanced chemical vapor deposition at low pressure and room temperature are reviewed. The in-situ techniques of plasma analysis and surface characterization (quadrupolar mass spectrometry, optical emission spectroscopy and ellipsometry) providing evidence of powder formation and the polymerization reactions based on the SinH2n- negative radicals electrically confined in the plasma sheath are described. The square wave modulation (SQWM) of the rf power is discussed as an efficient method of controlling the powder particle production with low particle-size dispersion. The properties of the powder particles determined by different structural characterization techniques providing their size and distribution, crystalline order and morphology, chemical composition and chemical bond vibrational characteristics, are analyzed and discussed[cat] Hom presenta una revisió sobre les partícules ultrafines de silici i els seus aliatges binaris i ternaris del sistema Si-B-C-N, produïdes en el nostre grup de recerca a partir dels gasos precursors silà, metà, diborà, amoníac i nitrogen, per dipòsit químic en fase vapor (CVD) reforçat per plasma, a baixa pressió i temperatura ambient. És descrita també la utilització de tècniques in situ d'anàlisi per plasma i de caracterització de superfícies (espectroscòpia de masses quadripolar, espectroscòpia òptica d’emissió i el·lipsometria), que donaren l’evidència de formació de partícules de pols i de reaccions de polimerització basades en radicals negatius SinH2n– confinats elèctricament en l’embolcall del plasma. La modulació d’ona quadrada (SQWM) de la font de rf és estudiada com un eficient mètode de control de la producció de partícules amb una petita dispersió de llurs dimensions. Finalment, hom analitza i discuteix les propietats de les partícules produïdes, determinades per diferents tècniques de caracterització, que permeteren obtenir llurs dimensions i distribució, ordre cristal·lí i morfologia, composició química i les característiques vibracionals dels enllaços químic

Megacrystals track magma convection between reservoir and surface

Active volcanoes are typically fed by magmatic reservoirs situated within the upper crust. The development of thermal and/or compositional gradients in such magma chambers may lead to vigorous convection as inferred from theoretical models and evidence for magma mixing recorded in volcanic rocks. Bi-directional flow is also inferred to prevail in the conduits of numerous persistently-active volcanoes based on observed gas and thermal emissions at the surface, as well as experiments with analogue models. However, more direct evidence for such exchange flows has hitherto been lacking. Here, we analyse the remarkable oscillatory zoning of anorthoclase feldspar megacrystals erupted from the lava lake of Erebus volcano, Antarctica. A comprehensive approach, combining phase equilibria, solubility experiments and melt inclusion and textural analyses shows that the chemical profiles are best explained as a result of multiple episodes of magma transport between a deeper reservoir and the lava lake at the surface. Individual crystals have repeatedly travelled up-and-down the plumbing system, over distances of up to several kilometers, presumably as a consequence of entrainment in the bulk magma flow. Our findings thus corroborate the model of bi-directional flow in magmatic conduits. They also imply contrasting flow regimes in reservoir and conduit, with vigorous convection in the former (regular convective cycles of ∼150 days at a speed of ∼0.5 mm s−1) and more complex cycles of exchange flow and re-entrainment in the latter. We estimate that typical, 1-cm-wide crystals should be at least 14 years old, and can record several (from 1 to 3) complete cycles between the reservoir and the lava lake via the conduit. This persistent recycling of phonolitic magma is likely sustained by CO2 fluxing, suggesting that accumulation of mafic magma in the lower crust is volumetrically more significant than that of evolved magma within the edifice.The work reported here has been partially supported by the National Science Foundation (Division of Polar Programs) under grant ANT1142083. The authors thank the Natural Environment Research Council (NERC) for access to the NERC Ion Microprobe Facility (Grant IMF453/1011) and Richard Hinton for invaluable help with SIMS analyses. Y.M. acknowledges support from the Cambridge Philosophical Society, the University of Cambridge Home and EU Scholarship Scheme, and the Philip Lake and William Vaughan Lewis funds from the Department of Geography, University of Cambridge. Y.M. also acknowledges support from ERC grant #279790.This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S0012821X14007833#

Refranes y dichos populares en árabe, castellano e inglés. Estudio contrastivo de los aspectos socioculturales

En este trabajo se analizan diferentes refranes y dichos populares en tres lenguas (árabe, castellano e inglés) desde el punto de vista sociocultural. Se da especial importancia a los referentes culturales que contienen los refranes seleccionados para estudiar el impacto de la traducción en el receptor del texto meta y aportar recomendaciones a la hora de traducir refranes sin equivalenciaEn aquest treball s'analitzen diferents refranys i dites populars en tres llengües (àrab, castellà i anglès) des d'un punt de vista sociocultural. Es dóna especial importància als referents culturals que apareixen als refranys seleccionats per a estudiar la reacció del receptor del text meta i aportar recomanacions a l'hora de traduir refranys sense equivalènciaThis work focuses its sociocultural analysis in several idioms in Arabic, Spanish and English. Cultural references of selected idioms are particularly important in order to study the reaction of receptors of the target text and give recommendations when translating idioms without equivalence in other languages

Detección e Identificación de los virus del papiloma humano. Caracterización de dos nuevas variantes

Los Papilomavirus Humanos (VPHs) son virus que causan enfermedades proliferativas en el epitelio de piel y mucosas. Su relación con el cáncer de cuello de útero se conoce desde la década de los 70 y actualmente está ampliamente aceptado que los papilomavirus humanos son el único agente etiológico causante del cáncer cervical. Constituyen un grupo de virus muy heterogéneo, dentro del cual destacan por cuestiones de tipo clínico algunos genotipos que presentan un alto potencial oncogénico y que son los causantes de la mayoría de los carcinomas invasores de cérvix. Se han desarrollado vacunas contra algunos de estos genotipos, y actualmente se están incluyendo en los programas nacionales de vacunación de un gran número de países. La tesis describe un trabajo de investigación que ha aportado tres aspectos novedosos que se presentan en los tres capítulos en los que está estructurada. En el primer capítulo se describe un nuevo sistema de detección e identificación de papilomavirus humanos de amplio espectro. El método está basado en la PCR (reacción en cadena de la polimerasa) y en RFLPs (análisis de fragmentos de restricción). Permite la identificación de los genotipos víricos presentes en las muestras clínicas con lesiones precursoras de cáncer de cuello de útero. De esta forma permite valorar el potencial evolutivo de las lesiones pre-cancerosas, ya que cada genotipo vírico presenta un nivel de riesgo específico. Asimismo, el método incorpora un mecanismo molecular desarrollado especialmente para el presente trabajo que permite detectar las eventuales inhibiciones de las reacciones de amplificación. En el segundo capítulo se describe la utilización del método presentado, para el estudio de 9.734 muestras clínicas procedentes de varios hospitales y centros sanitarios españoles. Se esta forma se consiguió detectar e identificar el genotipo vírico en un gran número de muestras y obtener información estadísticamente significativa respecto a la distribución de los diferentes genotipos en la población. También se estudió la relación entre la gravedad de la lesión y la edad con el genotipo presente en la muestra. En el tercer capítulo se describe el trabajo de caracterización de dos nuevas variantes detectadas con el método presentado en el primer capítulo. Este sistema de identificación permite la detección de un gran número de genotipos conocidos de papilomavirus, así como de variantes no descritas previamente. Esto permitió la detección de dos nuevos genotipos, que fueron secuenciados completamente y clasificados taxonómicamente como dos nuevos subtipos de tipos actualmente conocidos. En la presente tesis se ha desarrollado un sistema de detección e identificación de papilomavirus que ha sido comercializado como un producto para diagnóstico in vitro. Por otro lado, este sistema también ha sido comercializado como un servicio de laboratorio, consistente en la realización de una prueba y la emisión de un informe clínico. En total se han podido analizar aproximadamente unas 26.000 muestras clínicas utilizando este sistema El aspecto más destacado de este trabajo de tesis es el desarrollo de un sistema de detección e identificación de papilomavirus y su demostrada aplicabilidad clínica, así como su utilidad como método para la realización de estudios estadísticos sobre la distribución de genotipos víricos.The Human Papillomaviruses (HPVs) cause proliferative diseases in the epithelium of skin and mucous membranes. The relationship between them and cervical cancer has been known since the early '70s and now is widely accepted that human papillomaviruses are the only etiologic agent of cervical cancer. They are a very heterogeneous group of viruses. Some of them are very important so have a high oncogenic potential and they are responsible for most invasive cervical carcinomas. It has been developed vaccines against some of these genotypes, and currently are used in national immunization programs of many countries. The thesis describes a research project which has provided three new issues that arise in the three chapters in which it is structured. In the first chapter it is described a new system of detection and identification of human papillomavirus of broad spectrum. The system is based on PCR (polymerase chain reaction) and RFLPs (restriction fragment length polymorphism). It allows the identification of the viral genotypes present in clinical samples with precursor lesions of cervical cancer. Thus, it allows to assess the potential of the evolution of pre-cancerous lesions, because each viral genotype has a specific level of risk. Further, the method includes a molecular mechanism specially developed for this project to detect the eventual inhibition of the amplification reactions. In the second chapter it is described the utilization of the presented method to the analysis of 9.734 clinical samples from several hospitals and Spanish health centers. Thus, it was possible to detect and identify the viral genotype of a large number of samples and to obtain statistically significant information regarding the distribution of the different genotypes in the population. It was also studied the relation between the severity of the lesion and the age with the genotype present in the sample. In the third chapter it is described the project of the characterization of two new variants detected with the method presented in the first chapter. This identification method allows the detection of many papillomavirus of known genotype as well as variants not described previuosly. This allowed the detection of two new genotypes, which were completely sequenced and taxonomically classified as two new subtypes of the currently known types. In the present thesis it has been developed an identification and detection system of papillomavirus which has been commercialized as an in vitro diagnostic product. On the other hand, this system has also been commercialized as a laboratory service, consisting in the realization of a test and the emission of a clinical report. In total, it has been able to analyze about 26.000 clinical samples using this system. The highlight of this thesis is the development of an identification and detection system of papillomavirus and its proved clinical applicability, as well as its utility as a method for the realization of statistics studies about the distribution of viral genotypes