Insights into bacterial colony morphology evolution and diversification during infection development in cystic fibrosis

Tese de Doutoramento em Engenharia Biomédica.

Rol de la infección bacteriana en el desarrollo y progresión del cáncer prostático. Influence of bacterial infection in the development and progression of prostatitic cancer.

En la patogénesis del cáncer, factores microambientales como la inflamación están estrechamente vinculados al desarrollo y crecimiento tumoral, sustentando la clásica hipótesis de Virchow del origen del cáncer en sitios de inflamación crónica, la cual incitaría a carcinogénesis por múltiples factores. Estudios previos en este laboratorio evidenciaron en un modelo de prostatitis bacteriana agudo con E. coli, profundos cambios estromales semejantes al "estroma reactivo", con predominio de miofibroblasto, que se genera en el cáncer. En correlación, existe abundante evidencia obtenida en modelos experimentales animales confirmando que el microambiente estromal en el cual se desarrollan los tumores epiteliales influencia profundamente la progresión tumoral. El rol protagónico del estroma del huésped en el crecimiento neoplásico, también se ha demostrado inoculando la misma línea tumoral en diferentes tejidos y analizando su comportamiento en comparación con su implantación en el sitio anatómico original del tumor (implante ortotópico); otro factor clave en la repuesta del huésped al tumor está dado por el infiltrado de células inmunes que puede favorecer o limitar el crecimiento tumoral de acuerdo al perfil de citoquinas que secreten. Teniendo en cuenta estos antecedentes, este proyecto tiene como Objetivo General estudiar la influencia de la infección bacteriana crónica en la inducción y evolución del cáncer prostático. Para ello trabajaremos in vivo con dos formas de formas de Tumores Prostáticos, un Tumor Inducido por combinación del carcinógeno N-methyl-N-nitrosourea (MNU) y testosterona; el segundo mediante Transplante Ortotópico de células tumorales prostáticas MAT-LU. En ambos modelos se inducirá previamente una prostatitis bacteriana, a fin de estudiar los efectos de la prostatitis en la inducción del tumor en el primer modelo, y en la implantación de las células tumorales en el segundo. También se inducirá prostatitis después de establecido el tumor por ambos procedimientos, a fin de determinar si la prostatitis bacteriana modula la progresión neoplásica. Finalmente, proponemos un modelo in vitro que permita estudiar la interacción tumor/estroma separado de la influencia del sistema inmune. A tal fin se utilizarán co-cultivos combinando células tumorales con estromales modificadas de diferente modo. La Inducción de Tumores Prostáticos se realizará en ratas de la cepa Wistar adultas, en las cuales se inducirán lesiones displásicas y neoplásicas siguiendo protocolos de carcinogénesis prostática por MNU, para lo cual es necesario el tratamiento previo con acetato de ciprosterona y propionato de testosterona, seguido por administración crónica de testosterona. Los estudios con Transplante Ortotópico de células tumorales se realizarán en ratas Copenhagen. La influencia de la infección bacteriana en el desarrollo tumoral será investigada inyectando E. coli intraprostáticamente: Se realizará Análisis Macroscópico, de Parámetros Morfológicos de las lesiones tumorales, grado de malignidad, extensión e invasión de las lesiones de acuerdo a consensos internacionales, y Bioquímicos mediante análisis de la expresión, por IHQ y WB, de fosfatasa ácida, citoqueratina 8, Prostatic Binding Protein, PTEN (gen supresor tumoral) y el receptor de Andrógenos, todos parámetros de actividad y de transformación celular. También se evaluará apoptosis por TUNEL y proliferación celular. Los cambios del compartimiento estromal en respuesta al implante tumoral y la influencia de la inflamación bacteriana se evaluarán mediante análisis morfológico e inmunocitoquímico, caracterizando el fenotipo de las poblaciones celulares con a-actina, vimentina, calponina y tenascina. Se espera que los resultados aporten evidencias acerca de las interacciones bidireccionales entre células neoplásicas prostáticas y su entorno estromal, que en un futuro puedan servir como base para establecr estrategias para prevenir y/o modificar el crecimiento neoplásico.

Producción de factores de virulencia por fitopatógenos bacterianos de soja. Utilización de productos naturales como biocontrol. Production of virulence factors by soybean bacterial phytopathogens. The use of natural products as biocontrolers.

En Argentina el cultivo de soja ocupa el primer lugar en superficie sembrada. El 90% de la producción se obtiene en la zona central del pais. La siembra directa favorece la multiplicación y supervivencia de fitopatógenos causantes de tizón y pústula bacterianos. El tizón es producido por Pseudomonas syringae pv. glycinea observándose manchas marrones en las hojas. Produce gran variedad de toxinas: coronatina, faseolotoxina, siringomicina, tabtoxina, proteínas “nucleation ice”, entre otras, las cuales contribuyen a la clorosis y necrosis. En la infección, además, están involucrados exopolisacáridos (levano y alginato). La celulosa ha sido relacionada en la adhesión bacteriana y en la formación de biofilm. La pústula es causada por Xanthomonas axonopodis pv. glycines. Produce manchas pequeñas con una pequeña pústula de color claro. Libera enzimas como α-amilasa, proteasa, endo β-mannanasa, actividad peptolítica, que degradan componentes vegetales. Xantan, producido por X. axonopodis es uno de los componentes necesarios para la formación de biofilm. Este último es considerado un importante factor de virulencia porque proporciona una estrategia de colonización que otorga mayor resistencia a ambientes desfavorables, tolerancia a antimicrobianos, producción de metabolitos y exoenzimas, etc. Actualmente el control de bacterias fitopatógenas se realiza mediante pesticidas con alta toxicidad para los consumidores y el ambiente. Para evitar las bacteriosis en la práctica se sugiere la rotación de cultivos y utilizar semillas certificadas. Se están probando compuestos naturales derivados de plantas medicinales como pesticidas; estos se pueden dividir en varias categorías fitoquímicas. Varios estudios confirman la actividad antibacteriana, antifúngica y antiviral de estos productos. Extractos vegetales con alto contenido de flavonoides y aceite esenciales poseen una importante actividad antibacteriana. Además, algunos aceites esenciales podrían estar incidiendo en la liberación y/o producción de biofilm, exopolisacáridos y exoproteínas. La gran incidencia de las infecciones por fitopatógenos y las pérdidas económicas que estas acarrean hacen que su control presente grandes dificultades para la agricultura sustentable en soja de nuestro país. En este trabajo se propone estudiar los diferentes factores de virulencia de cepas bacterianas fitopatógenas y evaluar el rol que cumplen en el proceso de la enfermedad en cultivos de soja y desarrollar estrategias para el control de bacteriosis vegetales aplicando productos naturales aislados de plantas aromáticas. La correcta utilización de productos antimicrobianos de origen natural aplicados sobre el cultivo y/o sobre las semillas evitaría la dispersión de la enfermedad y la eliminación al medio ambiente de productos contaminantes no deseados. In Argentina, soybean cultivation occupies the first place; 90% of this cereal is produced in the central region of the country. Intensive tillage practices favour multiplication and survival of bacterial phytopathogens causing blight and pustule diseases. Pseudomonas syringae pv. glycinea produce several toxins like coronatine, faseolotoxine, siringomicine, tabtoxine and proteins of nucleation ice that contribute to the develop of chlorosis and necrosis, characteristic of bacterial blight. It also produces levan and alginate, cellulose and biofilm. Pustule disease is caused by Xanthomonas axonopodis pv glycines, which produce enzymes like α-amilase, protease, endo β-mannanase, peptolitic activity, xanthan and biofilm. Nowadays the control of phytopathogenic bacteria consists in the application of pesticides that are toxic for the environment and man. Natural products from medicinal plants are a new alternative for the treatment of phytopathogens. Researches made with phytochemical compounds (flavonoids, phenols, quinones, cummarines, essential oils, terpenes) support the antimicrobial activity of these natural products. What is more, these substances could suppress the biofilm, exoproteins and exopolisaccharides formation and release of them. The infections caused by phytopathogens provoke economical loses and its control presents big difficulties in our country. The proposal of this work is the characterization of phytopatoghenic strains, its virulence factors and the role they play in the disease process. The development of a new alternative for the control of vegetable bacteriosis using natural products obtained from aromatic plants and the correct application of them on sown fields or on seeds is also an objective in this work.

Some characteristics of hyperreactivity to bacterial lipopolysaccharide induced in mice by Trypanosoma cruzi infection

Mice infected with T. cruzi strain, acquire a high level of susceptibility to the effects of bacterial gram-negative LPS. The LD50 of adult female SW mice to LPS from S. typhosa, decreases from 450 to 2,5 mcg 10-12 days after T. cruzi infection. This hyperreactivity to LPS induced by T. cruzi presents all the characteristics of that found in infection caused by many other agents. During the acaute phase of experimental infection with T. cruzi Y strain, mice generally die with a hypovolemic shock very similar to that induced in uninfected animals injected with an adequate dose of bacterial endotoxin. There is evidence for and against the hypothesis that LPS absorbed from the instestinal tract may be involved in the mechanism of death of mice during the acute phase of T. cruzi infection.

Endocytosis-inducer adhesins produced by enteropathogenic serogroups of Escherichia coli participate on bacterial attachment to infant enterocytes

Enteropathogenic E. coli (EPEC) infection of Hep-2 cells preoceeds through bacterial attachment to cell surface and internalization of adhered bacteria. EPEC attachment is a prerequisite for cell infection and is mediated by adhesins that recognize carbohydrate-containing receptors on cell membrane. Such endocytosis-inducer adhesins (EIA) also promote EPEC binding to infant enterocytes, suggesting that EIA may have an important role on EPEC gastroenteritis.

Individual-based modelling of bacterial cultures to study the lag ohase

Els bacteris són la forma dominant de vida del planeta: poden sobreviure en medis molt adversos, i en alguns casos poden generar substàncies que quan les ingerim ens són tòxiques. La seva presència en els aliments fa que la microbiologia predictiva sigui un camp imprescindible en la microbiologia dels aliments per garantir la seguretat alimentària. Un cultiu bacterià pot passar per quatre fases de creixement: latència, exponencial, estacionària i de mort. En aquest treball s’ha avançat en la comprensió dels fenòmens intrínsecs a la fase de latència, que és de gran interès en l’àmbit de la microbiologia predictiva. Aquest estudi, realitzat al llarg de quatre anys, s’ha abordat des de la metodologia Individual-based Modelling (IbM) amb el simulador INDISIM (INDividual DIScrete SIMulation), que ha estat millorat per poder fer-ho. INDISIM ha permès estudiar dues causes de la fase de latència de forma separada, i abordar l’estudi del comportament del cultiu des d’una perspectiva mesoscòpica. S’ha vist que la fase de latència ha de ser estudiada com un procés dinàmic, i no definida per un paràmetre. L’estudi de l’evolució de variables com la distribució de propietats individuals entre la població (per exemple, la distribució de masses) o la velocitat de creixement, han permès distingir dues etapes en la fase de latència, inicial i de transició, i aprofundir en la comprensió del que passa a nivell cel•lular. S’han observat experimentalment amb citometria de flux diversos resultats previstos per les simulacions. La coincidència entre simulacions i experiments no és trivial ni casual: el sistema estudiat és un sistema complex, i per tant la coincidència del comportament al llarg del temps de diversos paràmetres interrelacionats és un aval a la metodologia emprada en les simulacions. Es pot afirmar, doncs, que s’ha verificat experimentalment la bondat de la metodologia INDISIM.

Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacterial strains routinely isolated in a clinical microbiology laboratory.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced in diagnostic microbiology laboratories for the identification of bacterial and yeast strains isolated from clinical samples. In the present study, we prospectively compared MALDI-TOF MS to the conventional phenotypic method for the identification of routine isolates. Colonies were analyzed by MALDI-TOF MS either by direct deposition on the target plate or after a formic acid-acetonitrile extraction step if no valid result was initially obtained. Among 1,371 isolates identified by conventional methods, 1,278 (93.2%) were putatively identified to the species level by MALDI-TOF MS and 73 (5.3%) were identified to the genus level, but no reliable identification was obtained for 20 (1.5%). Among the 1,278 isolates identified to the species level by MALDI-TOF MS, 63 (4.9%) discordant results were initially identified. Most discordant results (42/63) were due to systematic database-related taxonomical differences, 14 were explained by poor discrimination of the MALDI-TOF MS spectra obtained, and 7 were due to errors in the initial conventional identification. An extraction step was required to obtain a valid MALDI-TOF MS identification for 25.6% of the 1,278 valid isolates. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional phenotypic identification for most bacterial strains routinely isolated in clinical microbiology laboratories.

Multi-scale support vector algorithms for hot spot detection and modelling

The algorithmic approach to data modelling has developed rapidly these last years, in particular methods based on data mining and machine learning have been used in a growing number of applications. These methods follow a data-driven methodology, aiming at providing the best possible generalization and predictive abilities instead of concentrating on the properties of the data model. One of the most successful groups of such methods is known as Support Vector algorithms. Following the fruitful developments in applying Support Vector algorithms to spatial data, this paper introduces a new extension of the traditional support vector regression (SVR) algorithm. This extension allows for the simultaneous modelling of environmental data at several spatial scales. The joint influence of environmental processes presenting different patterns at different scales is here learned automatically from data, providing the optimum mixture of short and large-scale models. The method is adaptive to the spatial scale of the data. With this advantage, it can provide efficient means to model local anomalies that may typically arise in situations at an early phase of an environmental emergency. However, the proposed approach still requires some prior knowledge on the possible existence of such short-scale patterns. This is a possible limitation of the method for its implementation in early warning systems. The purpose of this paper is to present the multi-scale SVR model and to illustrate its use with an application to the mapping of Cs137 activity given the measurements taken in the region of Briansk following the Chernobyl accident.

CD14 expression on monocytes and TNF alpha production in patients with septic shock, cardiogenic shock or bacterial pneumonia.

OBJECTIVES: In patients with septic shock, circulating monocytes become refractory to stimulation with microbial products. Whether this hyporesponsive state is induced by infection or is related to shock is unknown. To address this question, we measured TNF alpha production by monocytes or by whole blood obtained from healthy volunteers (controls), from patients with septic shock, from patients with severe infection (bacterial pneumonia) without shock, and from patients with cardiogenic shock without infection. MEASUREMENTS: The numbers of circulating monocytes, of CD14+ monocytes, and the expression of monocyte CD14 and the LPS receptor, were assessed by flow cytometry. Monocytes or whole blood were stimulated with lipopolysaccharide endotoxin (LPS), heat-killed Escherichia coli or Staphylococcus aureus, and TNF alpha production was measured by bioassay. RESULTS: The number of circulating monocytes, of CD14+ monocytes, and the monocyte CD14 expression were significantly lower in patients with septic shock than in controls, in patients with bacterial pneumonia or in those with cardiogenic shock (p < 0.001). Monocytes or whole blood of patients with septic shock exhibited a profound deficiency of TNF alpha production in response to all stimuli (p < 0.05 compared to controls). Whole blood of patients with cardiogenic shock also exhibited this defect (p < 0.05 compared to controls), although to a lesser extent, despite normal monocyte counts and normal CD14 expression. CONCLUSIONS: Unlike patients with bacterial pneumonia, patients with septic or cardiogenic shock display profoundly defective TNF alpha production in response to a broad range of infectious stimuli. Thus, down-regulation of cytokine production appears to occur in patients with systemic, but not localised, albeit severe, infections and also in patients with non-infectious circulatory failure. Whilst depletion of monocytes and reduced monocyte CD14 expression are likely to be critical components of the hyporesponsiveness observed in patients with septic shock, other as yet unidentified factors are at work in this group and in patients with cardiogenic shock.

Pullulation bactérienne de l'intestin grêle [Small intestine bacterial overgrowth]

Small intestine bacterial overgrowth (SIBO) is a condition characterised by nutrient malabsorption and excessive bacteria in the small intestine. It typically presents with diarrhea, flatulence and a syndrome of malabsorption (steatorrhea, macrocytic anemia). However, it may be asymptomatic in the eldery. A high index of suspicion is necessary in order to differentiate SIBO from other similar presenting disorders such as coeliac disease, lactose intolerance or the irritable bowel syndrome. A search for predisposing factor is thus necessary. These factors may be anatomical (stenosis, blind loop), or functional (intestinal hypomotility, achlorydria). The hydrogen breath test is the most frequently used diagnostic test although it lacks standardisation. The treatment of SIBO consists of eliminating predisposing factors and broad-spectrum antibiotic therapy.

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets.

An ammonium chloride erythrocyte-lysing procedure was used to prepare a bacterial pellet from positive blood cultures for direct matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry analysis. Identification was obtained for 78.7% of the pellets tested. Moreover, 99% of the MALDI-TOF identifications were congruent at the species level when considering valid scores. This fast and accurate method is promising.

Spot inversion in the Heston model

We analyse the Heston stochastic volatility model under an inversion of spot. The result is that under the appropriate measure changes the resulting process is again a Heston type process whose parameters can be explicitly determined from those of the original process. This behaviour can be interpreted as some measure of sanity of the Heston model but does not seem to be a general feature of stochastic volatility processes.