Detection of Helicobacter pylori Microevolution and Multiple Infection, and Genomic Analysis of Helicobacter pylori Strains

[eng] In the past decades, Helicobacter pylori has received the attention of many researchers because of its known relation with gastric cancer. Although many studies have tried to decipher the exact relation between the bacteria and cancer state, and several virulence factors have been discovered, an exact answer has not been found yet. Further work should be made in order to study more accurately the genome of this bacterium and to understand its precise involvement. The bacterium is characterised for a highly genetic diversity, meaning it is continuously changing in order to adapt itself to its hostile niche, the human stomach. Infection by H. pylori is estimated to affect half of the world’s population, being more extended in developing countries than in developed ones, possibly due to the high consumption of antibiotics and the increased level of sanitation in the latest. It has been demonstrated that the gastric lumen can be colonized by more than just one strain of the bacterium, sometimes these strains could have evolved from the same ‘mother’ strain, or they could come from unrelated strains. The study of these situations is important in order to elucidate if there is just one strain who is responsible for starting the pathogenic cascade, and what are the specific differences between the different strains that inhabit the human stomach. On the first work of this thesis, our group studied the usefulness of six housekeeping genes for the detection of H. pylori infection and the characterization of various strains isolated from gastric isolates, studying as well their phylogeny. In some cases, the distance value between the strains was high, indicating and event of multiple infection. In other cases, small differences were found between clones, suggesting events of microevolution rather than multiple infection. This work was further extended with the study of the usefulness of amplicon sequencing of these housekeeping genes in the detection of microevolution and mixed infections from gastric biopsies of patients with dyspeptic symptoms and different histopathological findings (from atrophy to adenocarcinoma). Five gastric biopsies from four patients infected by H. pylori were involved in this study. We detected in all the analyzed gastric biopsies multiple H. pylori infections with a predominant strain. These results suggest that H. pylori colonizes the human stomach through diverse infection circumstances that lead to a gastric multi-infection with a predominant strain together alongside other minority strains. Furthermore, it was shown that mixed infections are the main status in the colonization of the human gastric mucosa. The last part of this thesis started with a preliminary study of 51 complete sequenced H. pylori genomes and further focused on three genomes obtained from the same patient in order to analyse and compare them. Particularly, these isolates were sampled at the same time from a stomach with adenocarcinoma, one strain was from the non- tumoral tissue, and the other two were isolated from the tumoral tissue. They all lacked from the most noticeable virulence factor, the cag pathogenicity island; one of the most studied and the main factor related to the malignancy of the bacterium. On the other hand, we found differences in the genotype of the vacuolating cytotoxin gene (vacA) and in genes related with urease, the outer membrane and flagella. Despite the contributions made in this thesis, further studies are needed to find better genetic markers of H. pylori related to virulence and progression to gastric cancer.[cat] Helicobacter pylori és el focus d’atenció de molts estudis a causa de la seva coneguda relació amb el càncer gàstric. Encara que molts estudis han tractat de desxifrar la relació exacta entre el bacteri i la progressió del càncer, i s'han descobert diversos factors de virulència, no s'ha trobat una resposta exacta. En la primera part d'aquesta tesi, es va estudiar la utilitat de sis gens conservats per la detecció de la infecció per H. pylori i la caracterització de diverses soques aïllades de biòpsies gàstriques, estudiant-se també la seva filogènia. En alguns casos, el valor de la distància entre les soques era alt, fet indicatiu d’un esdeveniment d'infecció múltiple. En altres casos, es van trobar petites diferències entre els clons, el que suggereix esdeveniments de microevolució en lloc d’infecció múltiple. Aquesta tesi es va ampliar amb l'estudi de la utilitat de la seqüenciació d'amplicons d'aquests gens conservats en la detecció de microevolució i infeccions múltiples en biòpsies gàstriques de pacients amb símptomes dispèptics. En aquest estudi es van analitzar cinc biòpsies gàstriques de quatre pacients infectats per H. pylori. En totes les biòpsies gàstriques analitzades es van detectar infeccions múltiples per H. pylori amb una soca predominant. Aquests resultats suggereixen que H. pylori colonitza l'estómac humà mitjançant diverses circumstàncies d'infecció que condueixen a una infecció múltiple gàstrica amb una soca predominant juntament amb altres soques minoritàries. L'última part d'aquesta tesi va començar amb l’estudi preliminar de 51 genomes complets d’H. pylori i es va centrar després en l’estudi i comparació de tres genomes obtinguts del mateix pacient. Específicament, aquestes soques van ser aïllades alhora d’un estómac amb adenocarcinoma, on una soca provenia del teixit no tumoral i les altres dues del teixit tumoral. Totes mancaven del factor de virulència més destacat, l'illa de patogenicitat cag; un dels factors més estudiats i el més relacionat amb la malignitat del bacteri. Per una altra banda, vam trobar diferències en el genotip del gen vacA i en gens relacionats amb la ureasa, la membrana externa i els flagels

Sistema y procedimiento de inspección de superficies de estructuras micro y nanomecánicas

Sistema de inspección de superficies dispuesto para detectar características de desplazamiento relativo y/o de vibración de diversos puntos de una pluralidad de elementos (51) que forman parte de una estructura mecánica (5), comprendiendo dicho sistema: una fuente de luz (1) dispuesta para generar, al menos, un haz de luz (11); un detector sensible a la posición (2) dispuesto para recibir el haz de luz cuando es reflejado fuera de la estructura mecánica (5) y para generar, al menos, una señal de salida en respuesta a la recepción de dicho haz de luz; un sistema de control electrónico (3); un medio de exploración (4) para el desplazamiento relativo de dicho haz de luz con relación a la estructura mecánica (5) con el fin de explorar dicha estructura mecánica con el haz de luz, siguiendo las instrucciones del sistema de control electrónico (3); caracterizado porque dicho sistema de control electrónico (3) está dispuesto para controlar el medio de exploración (4) con el fin de desplazar el haz de luz por la estructura mecánica a lo largo de una primera trayectoria (A) con objeto de detectar una pluralidad de posiciones de referencia subsiguientes (C), cada una en un elemento, a lo largo de dicha primera trayectoria (A), en el que dicho sistema de control electrónico (3) está asociado operativamente con dicho detector sensible a la posición (2) para determinar dichas posiciones de referencia (C) como resultado de un análisis de, al menos, una señal de salida de dicho detector sensible a la posición (2); en el que dicho sistema de control electrónico (3) está dispuesto además para controlar el medio de exploración (4) para desplazar el haz de luz por la estructura mecánica a lo largo de una pluralidad de segundas trayectorias (B), estando asociada cada una de dichas segundas trayectorias (B) con una de dichas posiciones de referencia (C); dicho sistema de control electrónico está dispuesto además para obtener, durante el desplazamiento del haz de luz a lo largo de cada una de dichas segundas trayectorias (B), una pluralidad de salidas de señales de posición de dicho detector sensible a la posición (2).Peer reviewedConsejo Superior de Investigaciones Científicas (España)T3 Traducción de patente europe

Functional stability and community dynamics during spring and autumn seasons over 3 years in Camargue microbial mats

Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0-2, 2-4, and 4-6 mm). To assess bacterial diversity in the mats, amplicons of the V1-V2 region of the 16S rRNA gene were sequenced. The community's functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria ( 94%), followed by Archaea ( 4%) and Eukarya ( 1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70-80% of the total population detected. The phylum Euryarchaeota represented 80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0-2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0-2 mm) than in the lower layers (2-4 and 4-6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat

Real energy payback time and carbon footprint of a GCPVS

Grid connected PV systems, or GCPVS, produce clean and renewable energy through the photovoltaic e ect in the operation stage of the power plant. However, this is the penultimate stage of the facilities before its dismantlement. Before starting generating electricity with zero CO2 emissions, a negative energy balance exists mainly because of the embodied energy costs of the PV components manufacturing, transport and late dismantlement. First, a review of existing studies about energy life cycle assessment (LCA) and Carbon Footprint of PV systems has been carried out in this paper. Then, a new method to evaluate the Real Energy Payback Time (REPBT), which includes power looses due to PV panels degradation is proposed and di erences with traditional Energy Payback Time are analysed. Finally, a typical PV grid connected plant (100 kW nominal power) located in Northern Spain is studied in these sustainability terms. This facility has been firstly completely modelled, including PV modules, inverters, structures and wiring. It has been also considerated the energy involved in the replacement of those components with shorter lifespan. The PV panels degradation has been analysed through the comparison of normalised flash test reports on a significant sample of the installed modules before and 5 years after installation. Results show that real PV degradation a ect significantly to the Energy Payback Time of the installation increasing slightly a 4:2% more the EPBT value for the case study. However, along a lifespan of 30 years, the GCPVS under analysis will return only 5:6 times the inverted energy on components manufacturing, transport and installation, rather than the expected 9:1 times with the classical estimation

Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment

Gut microbial structure in animals depends on the host, dietary habits and local environment. A random event, dietary change or antibiotic treatment may alter the gut environment with possible repercussions for the bacterial community composition and functionality and ultimately host fitness. The present study was focused on the composition, structure and functionality of gut microbiota in Reticulitermes grassei and the data obtained was compared with sequence surveys of three other Reticulitermes species. Each Reticulitermes species had a significantly different bacterial gut microbiota (pairwise significance tests using the Kolmogorov-Smirnov test), but a similar pattern of distribution (P-test in weighted Unifrac). The core gut microbiota from the analyzed Reticulitermes species contained 16 bacterial operational taxonomic units. Enzymes (KO) were detected from 14 pathways related to carbohydrate metabolism. R. grassei and R. hesperus, based on relative abundance of KO, had the most similar carbohydrate pathway patterns. In addition, we described the gut microbiota and functionality pathways in R. grassei after a 7-day dietary shift and antibiotic (ciprofloxacin) treatment. Both factors, but above all the antibiotic, altered the relative abundance of certain microbial groups, although the changes were not statistically significant (P-test in weighted Unifrac). The cellulose diet enhanced the carbohydrate pathways related to propanoate, butanoate, ascorbate, and glyoxylate metabolism. The antibiotic treatment affected galactose metabolism, the citrate cycle and inositol phosphate metabolism. Those functional changes may be related to changes in the abundance of several bacterial groups. Our findings provide insights into the stability of the gut microbiota in R. grassei and a resilience response to dietary shift or antibiotic treatment disturbance after 7 days

Net Energy Balance and Smart Grids in Spain: Integration with PV Systems

En este documento se presentan las principales configuraciones y reglamentos técnicos en España sobre Net Energy Balance Systems y Smart Grids. Esta falta de instalaciones es bastante interesante para los futuros desarrollos de fuentes de energía verde, especialmente fotovoltaicas. Los principales beneficios son la reducción de las pérdidas de energía en el sistema de distribución, la optimización de los recursos energéticos y un mejor seguimiento de la oferta de energía y la demanda de energía. Las redes inteligentes y los sistemas de equilibrio energético neto son las últimas tendencias en generación y distribución de energía eléctrica. Sus beneficios están ampliamente demostrados y contribuyen a reducir las emisiones de CO2 a la atmósfera y aumentar las tasas de eficiencia. La falta de apoyo público a la generación de energía fotovoltaica hace obligatorio buscar nuevos puntos de vista. Sin piensos en las políticas arancelarias, las enormes plantas fotovoltaicas no son atractivas hoy en día. Debemos centrarnos en los sistemas pequeños implementados en Smart Grids y apoyados con estrategias de Net Energy Balance. Esta es otra manera de apoyar la generación de energía verde y tiene grandes beneficios para los usuarios domésticos

Sun‐trackers profitability analysis in Spain

pp.1010-1022El objetivo principal de este estudio es analizar el rendimiento de los dispositivos de seguimiento solar en comparación con los sistemas de placaplana fija utilizando datos de un software de predicción de irradiación ampliamente utilizado (PVGIS). Analizamos los parámetros típicos comosuma diaria y mensual de irradiación global (HdandHm) o la producción media diaria y mensual estimada de electricidad (EhandEm) y también sus costos asociados y requisitos de tierra (generalmente descritos por la relación de cobertura del suelo,GCR ). Se observó que la influencia de estos dos últimos parámetros es bastante importante para el cálculo del tiempo de amortización de toda la instalación. Como resultado final, se concluye que aunque el rastreador de doble eje permite el máximo rendimiento energético, un 38% más alto que un sistema fijo en promedio, si tenemos en cuenta el valor GCR y calculamos la relación de rendimiento super-cara, la más eficiente configuración es el rastreador solar de eje horizontalS

Performance Indicators for Sun-Tracking Systems: A Case Study in Spain

pp. 292-302Current PV cells technology takes advantage mainly from beam radiation. In this context the sun-trackers are such devices for efficiency improvement. On the other hand, projected shadows between devices make mandatory to increase the distances between mounting systems. Thus, the land’s capacity for mounting PV panels can be dramatically decreased. This fact conducts us to wonder where the optimum efficient point is. First, in this paper different types of sun-tracking systems are classified according to the movement they perform (cinematic classification). Further, three real PV installations-fixed, horizontal-axis tracking and dual-axis mount tracking—located in the same geographical area in Spain (they are approximately under the same weather conditions) are analyzed. These installations have been studied in order to establish which one is the most efficient and affordable—Specific Energy Production (SEP) and Performance Ratio (PR) analysis. PVGIS solar radiation estimate tool has been used for comparing the theoretical radiation potential on each plant. The land requirements have been considered in the analysis of the Ground Cover Ratio (GCR) and the Surface Performance Ratio (SPR). Moreover, comparing three main financial indicators let us carry out a financial study: Payback Time (PBT), Net Present Value (NPV) and Internal Rate of Return (IRR). In the case study, final annual energetic results demonstrate that the dual-axis plant shows a relevant SEP advantage, but if we take into account the land occupied for this sort of devices we find much more profitable the horizontal-axis sun-tracking system, with a SPR value 4.24% higher than the fixed system we have studied. Its PBT is also a 22% lower than the dual-axis tracking installationS

Capacity of the CCC-2 to discriminate ASD from other neurodevelopmental disorders

The Children’s Communication Checklist (CCC-2) has demonstrated its usefulness as an instrument to assess discrepancies between the use of structural dimensions of language and the pragmatic and sociointeractive uses of language. The aims of the present paper are: (1) to test the capacity of the Galician adaptation of the CCC-2 to discriminate the linguistic profiles of children with different disorders and (2) to test whether the capacity of the CCC-2 to discriminate the linguistic abilities of children with different disorders is the same at different ages: earlier development and later development. The sample is of 117 children previously diagnosed with different disorders: autism spectrum disorder (ASD), developmental language disorder (DLD), attention deficit with hyperactivity disorder (ADHD), Down syndrome children (DS) and typically developing children (TD). The children were divided into two different age groups: from 4 to 6 and from 7 to 16 years of age. The results indicate that the Galician CCC-2 (1) accurately identified children with and without communicative impairments, (2) distinguished between profiles with a predominance of pragmatic (ASD and ADHD) and structural disorders (DS and DLD) and (3) distinguished between different profiles of pragmatic impairment. The CCC-2 equally identified these profiles at both earlier and later ages. The Galician CCC-2 seems to be a useful instrument for differentiating among different clinical groups and for assessing pragmatic disorders from an early age, which can be valuable for planning early interventionS

Enumeration of locally Brunovsky linear systems over C(S1)-modules. A procedure

pp. 72-76In this paper we describe a procedure to visit all feedback classes of locally Brunovsky linear system over fixed R=C(S1) the ring of real continuos functions defined on the unit circle. Furthermore, we give the exact number of such classes throughout partitions of integers, binary strings and colored Ferrers diagrams.S