Yes / Peptidyl-prolyl isomerase (PPIase) lipoproteins have been shown to influence the virulence of a number of Gram-positive bacterial human and animal pathogens, most likely through facilitating the folding of cell envelope and secreted virulence factors. Here, we used a proteomic approach to demonstrate that the Streptococcus equi PPIase SEQ0694 alters the production of multiple secreted proteins, including at least two putative virulence factors (FNE and IdeE2). We demonstrate also that, despite some unusual sequence features, recombinant SEQ0694 and its central parvulin domain are functional PPIases. These data add to our knowledge of the mechanisms by which lipoprotein PPIases contribute to the virulence of streptococcal pathogens.

<p>Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation. </p><p>The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. <i>Rickettsia prowazekii</i>, the causative agent of epidemic typhus and <i>Helicobacter pylori</i>, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in <i>Rickettsia</i>. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in <i>H. pylori</i> were studied.</p><p>The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) <i>Rickettsia</i>, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in <i>R. conorii</i> indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the <i>H. pylori </i>carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in <i>H. pylori</i> were studied, of which antigenicity and gene location were identified as the strongest factors. </p><p>In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research.</p>

Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation. The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. Rickettsia prowazekii, the causative agent of epidemic typhus and Helicobacter pylori, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in Rickettsia. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in H. pylori were studied. The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) Rickettsia, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in R. conorii indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the H. pylori carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in H. pylori were studied, of which antigenicity and gene location were identified as the strongest factors. In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research.

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Title from first page of PDF document. Includes bibliographical references.

L'objectif principal de ce travail etait d'explorer les bactéries pathogènes que recèle le tube digestif des gorilles. Pour ce faire, un total de 48 échantillons de selles, provenant du Cameroun, appartenant à 21 gorilles ont été analysés. D'abord la culturomique et le pyroséquençage ont été utilisés pour évaluer exhaustivement la diversité bactérienne. En appliquant la culturomique, 86 conditions de culture dont des milieux fabriqués à base de plantes tropicales, sur un échantillon de selles de gorille, 12 800 colonies microbiennes ont été isolées et testées, et 147 espèces bactériennes identifiées. De nombreux pathogènes opportunistes ont été observés, dont 8 qui sont fréquemment associés à des maladies chez l'homme: Mycobacterium bolletii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, Escherichia coli, Staphylococcus aureus et Clostridium botulinum. En utilisant la PCR en temps réel pour cribler des pathogènes bactériens dans les 48 échantillons de selles de gorilles, des bactéries fastidieuses telles que Bartonella spp. Borrelia spp., Coxiella burnetii, Tropheryma whipplei ont été observées. Nous avons estimé la prévalence de ces agents pathogènes qui varie entre 4,76% et 85,7%. Ce travail a permis de savoir que l'homme et le gorille ont en commun plusieurs espèces bactériennes dont des pathogènes émergents. Par conséquent, les gorilles sauvages peuvent servir de réservoir et de source pour l'émergence et/ou la réémergence des bactéries pathogènes pour l'homme. / The main objective of this work is to explore the gorilla's potential role as a reservoir for pathogenic bacteria. We used both microbial culturomics and pyrosequencing to analyze the gorilla gut bacteria. By applying culturomics to one index gorilla, we tested 12,800 colonies and identified 147 different bacterial species, including 5 new species. Many opportunistic human pathogens were observed, including 8 frequently associated with human disease: Mycobacterium bolletii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, Escherichia coli, Staphylococcus aureus and Clostridium botulinum. Using specific real-time PCR on 48 gorilla fecal samples, we also observed the fastidious pathogens Bartonella spp. Borrelia spp., Coxiella burnetii, Tropheryma whipplei. Using microsatellite analysis of the gorilla samples, we estimated that the prevalence of these pathogens was between 4.76% and 85.7%. Therefore, the gorilla shares many bacterial pathogens with humans, which suggests that wild gorillas might be a reservoir for the emergence and/or reemergence of these pathogens, especially in areas where human and gorilla habitats overlap and because of the increasing presence of humans in the African equatorial forests.

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Tesis por compendio / [EN] Persimmon (Diospyros kaki L.) 'Rojo Brillante' is an astringent variety characterised by good growing conditions, excellent colour, size, sensory characteristics and good nutritional properties. In the last decade, its production has grown substantially in Spain given the application of high levels of CO2 to remove astringency while firmness is preserved. This technology has also increased its potential as a fresh-cut commodity. However, physical damage during processing result in degradation of the colour and firmness of the product and a higher susceptibility to microbial spoilage that significantly reduces the fruit's shelf life. The objective of the present thesis was to develop optimum procedures for processing and marketing 'Rojo Brillante' persimmon into a fresh-cut product with the maximum shelf life and best physicochemical, nutritional, sensory and microbiological quality. Firstly, the objective was to evaluate the effect of the maturity stage (MS) at harvest, storage time at 15 ºC before processing, and the application of different antioxidant treatments on enzymatic browning, sensory and nutritional quality of fresh-cut 'Rojo Brillante' persimmon during storage at 5 ºC. Concentrations of 10 g L-1 ascorbic acid (AA) or 10 g L-1 citric acid (CA) controlled tissue browning and maintained the visual quality of fresh-cut persimmon above the limit of marketability for 6-8 storage days at 5 ºC, depending on the MS. However, these acidic solutions reduced fruit firmness as compared to control samples. Further studies showed that the combination of these antioxidants with 10 g L-1 CaCl2 maintained firmness of the persimmon slices within the same range as the control samples. In another work, the application of 1-methylcyclopropene (1-MCP) allowed to process fruits after 45 days of storage at 1 ºC with commercial firmness and the antioxidant solution (10 g L-1 CA + 10 g L-1 CaCl2) extended the limit of marketability up to 9 days of storage at 5 ºC. Different controlled atmosphere conditions in combination with AA or CA dips were also evaluated as a first step to select optimum O2 and CO2 concentrations for modified atmosphere packaging (MAP) of fresh-cut 'Rojo Brillante' persimmons. Overall, the combination of antioxidant dips and a controlled atmosphere composed of 5 kPa O2 (balance N2) was proved to be the most effective combination to control enzymatic browning. This atmosphere maintained the visual quality of persimmon slices within the limit of marketability during 7- 9 days at 5 ºC. On the contrary, high CO2 concentrations (10 or 20 kPa) induced darkening in some tissue areas, associated with a flesh disorder known as 'internal flesh browning'. Later studies confirmed the beneficial effect of an active MAP in 5 kPa O2 compared to passive MAP to improve the visual quality of fresh-cut 'Rojo Brillante' persimmon, showing a synergic effect with the antioxidant dip (10 g L-1 CA + 10 g L-1 CaCl2). Antioxidant edible coatings were prepared from whey protein isolate (WPI), soy protein isolate (SPI), hydroxylpropyl methylcellulose (HPMC) and apple pectin as the polymeric matrix. All edible coatings were amended with the antioxidant combination selected (10 g L-1 CA + 10 g L-1 CaCl2). All the edible coatings tested proved effective to control enzymatic browning of persimmon slices. However, the samples treated with the HPMC- and pectin- based coatings were scored with a better visual quality that the rest of the treatments. In general, free radical scavenging activity and total carotenoid content increased in late-season persimmons; whereas, processing (cutting and storage at 5 ºC), antioxidant dips, controlled atmosphere storage or edible coatings had no clear effect on nutritional quality (vitamin C, free radical scavenging activity, total phenolic content, and carotenoids) of fresh-cut persimmons. / [ES] El caqui persimmon (Diospyros kaki L.) 'Rojo Brillante' es un cultivar astringente que presenta unas propiedades organolépticas y nutricionales excelentes. En la última década, su cultivo en el área mediterránea de España se ha incrementado de manera exponencial con el desarrollo de la tecnología que permite eliminar la astringencia, manteniendo la firmeza del mismo. Esta nueva forma de presentación, aporta numerosas ventajas, entre la que se incluye la posibilidad de ser comercializado como fruta fresca cortada. Sin embargo, el éxito comercial del producto está limitado por el pardeamiento enzimático, la pérdida de firmeza y al crecimiento microbiano. En este contexto, el objetivo de la Tesis ha sido el desarrollo de caqui 'Rojo Brillante' fresco cortado mediante un enfoque que integra el estudio de las características del producto en el momento del procesado y de distintas tecnologías que mantengan la calidad físico-química, sensorial, nutricional y microbiológica del producto durante un periodo que permita su comercialización. En primer lugar, se evaluó el efecto del estado de madurez (MS) en el momento de recolección, el tiempo de almacenamiento a 15 ºC antes del procesado y la aplicación de diferentes antioxidantes en el pardeamiento enzimático y la calidad sensorial y nutricional del caqui 'Rojo Brillante' cortado y almacenado a 5 ºC. La aplicación de 10 g L-1 de ácido ascórbico (AA) ó 10 g L-1 ácido cítrico (CA) controló el pardeamiento enzimático y mantuvo la calidad visual del caqui por encima del límite de comercialización entre 6 y 8 días de almacenamiento a 5 ºC, dependiendo del MS. Sin embrago, la aplicación de estos antioxidantes redujo de manera significativa la firmeza del fruto respecto al control. La combinación de estos antioxidantes con 10 g L-1 de CaCl2 permitió mantener la firmeza en el mismo rango que las muestras control. En un trabajo posterior, la aplicación de 1-metilciclopropeno (1-MCP) permitió procesar caqui almacenado 45 días a 1 ºC con una buena firmeza comercial y el tratamiento antioxidante (10 g L-1 CA + 10 g L-1 CaCl2) consiguió alcanzar un límite de comercialización del producto de 9 días a 5 ºC. La evaluación de distintas atmósferas controladas en combinación con tratamientos antioxidantes (AA o CA), como paso previo al envasado en atmósfera modificada (MAP) del caqui, mostró como más efectiva en el control del pardeamiento enzimático la atmósfera compuesta por 5 kPa O2 (balance N2). Esta atmósfera mantuvo la calidad visual del caqui cortado dentro del límite de comercialización durante 7-9 días a 5 ºC. Por el contrario, la aplicación de altas concentraciones de CO2 (10 ó 20 kPa) dio lugar a un pardeamiento en ciertas zonas de la pulpa que se conoce como 'internal flesh browning'. Estudios posteriores confirmaron el efecto beneficioso del envasado de caqui cortado y tratado con solución antioxidante (CA-CaCl2) en una MAP activa de 5 kPa O2 en la calidad visual del fruto frente a la aplicación de una MAP pasiva. El desarrollo de recubrimientos comestibles con capacidad antioxidante se realizó mediante la incorporación de antioxidantes (10 g L-1 CA + 10 g L-1 CaCl2) a formulaciones a base de proteína de suero lácteo (WPI), proteína de soja (SPI), hidroxipropilmetilcelulosa (HPMC) y pectina. Todos los recubrimientos fueron efectivos controlando el pardeamiento enzimático del caqui cortado, siendo las muestras recubiertas con HPMC y pectina las mejor evaluadas visualmente. En general, el procesado, la aplicación de antioxidantes, el envasado en atmósferas controladas y los distintos recubrimientos comestibles estudiados, si bien no mostraron un efecto claro en los parámetros de calidad nutricional evaluados, no tuvieron un efecto negativo en los mismos. Por otra parte, los frutos cosechados a final de campaña tuvieron mayor actividad antioxidante y contenido en carotenoides. / [CA] El caqui persimmon (Diospyros kaki L.) 'Rojo Brillante' és un cultiu astringent que presenta unes propietats organolèptiques i nutricionals excel¿lents. En la última dècada, el seu cultiu en l'àrea mediterrània d'Espanya s'ha incrementat de manera exponencial amb el desenvolupament de la tecnologia que permet eliminar l'astringència, mantenint la fermesa del mateix. Esta nova forma de presentació, aporta un gran nombre d'avantatges, entre els quals s'inclou la possibilitat de comercialitzar-lo com fruita fresca processada. No obstant, l'èxit comercial del producte està limitat per pardetjament enzimàtic, la pèrdua de fermesa i el creixement microbià. L'objectiu de la Tesis ha estat en el desenvolupament de caqui 'Rojo Brillante' tallat en fresc mitjançant un enfocament que integra l'estudi de les característiques del producte en el moment del processat i de diferents tecnologies en el manteniment de la qualitat físico-química, sensorial, nutricional i microbiològica del producte durant un període que permeta la seua comercialització. En primer lloc, es va avaluar l'efecte de l'estat de maduresa (MS) en el moment de recol¿lecció, el temps d'emmagatzemament a 15ºC abans del processat i l'aplicació de diferents tractaments antioxidants en el pardetjament enzimàtic i la qualitat sensorial i nutricional del caqui 'Rojo Brillante' tallat i emmagatzemat a 5 ºC. L'aplicació de 10 g L-1 d'àcid ascòrbic (AA) o 10 g L-1 d'àcid cítric (CA) va controlar el pardetjament enzimàtic i va mantenir la qualitat visual del caqui per damunt del límit de comercialització entre 6-8 dies d'emmagatzemament a 5 ºC, depenent del MS. No obstant, l'aplicació d'antioxidants va reduir de manera significativa la fermesa del fruit comparat amb el control. La combinació d'aquestos antioxidants amb 10 g L-1 de CaCl2 va permetre mantenir la fermesa en el mateix rang que les mostres control. En un treball posterior, l'aplicació de 1-metilciclopropeno (1-MCP) va permetre processar caqui emmagatzemat 45 dies a 1 ºC amb una bona fermesa comercial i a més, el tractament antioxidant (10 g L-1 CA + 10 g L-1 CaCl2) va aconseguir un límit de comercialització del producte tallat de 9 dies a 5 ºC. L'avaluació de diferents atmosferes controlades en combinació amb tractaments antioxidants (AA o CA), com a pas previ a l'envasament en atmosfera modificada (MAP) del caqui 'Rojo Brillante, va mostrar com a més efectiva en el control del pardetjament enzimàtic l'atmosfera composta per 5 kPa O2 (balanç N2). Aquesta atmosfera va mantenir la qualitat visual del caqui tallat dins del límit de comercialització durant 7-9 dies a 5 ºC. Per contra, l'aplicació d'altes concentracions de CO2 (10 ó 20 kPa) va donar lloc a un pardetjament en certes zones de la polpa, el qual és conegut com 'internal flesh browning'. Estudis posteriors van confirmar l'efecte beneficiós de l'envasament de caqui tallat i tractat amb solució antioxidant (CA-CaCl2) en una MAP activa de 5 kPa O2 millorant la qualitat visual de la fruita front a l'aplicació de una MAP passiva. El desenvolupament de recobriments comestibles amb capacitat antioxidant es va realitzar mitjançant la incorporació d'antioxidants (CA-CaCl2) en formulacions a base de proteïna de sèrum làctic (WPI), proteïna de soia (SPI), hidroxipropilmetilcel-lulosa (HPMC) i pectina. Tots els recobriments van ser efectius controlant el pardetjament enzimàtic del caqui tallat. No obstant, les mostres recobertes amb HPMC i pectina van ser millor avaluades visualment que la resta de tractaments. En general, el processat, l'aplicació d'antioxidants, l'envasament en atmosferes controlades i els distints recobriments comestibles estudiats, si bé no van mostrar un efecte clar en els paràmetres de la qualitat nutricional avaluats, no van tindre un efecte negatiu en els mateixos. Per altra banda, els fruits recol¿lectats a final de temporada van tenir major activitat antioxidant i contingut en / Sanchís Soler, E. (2016). Effect of processing on the physicochemical, sensory, nutritional and microbiological quality of fresh-cut 'Rojo Brillante' persimmon [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/62588 / Compendio