Isolation of recombinant antibody fragments (scFv) by phage display technology for detection of almond allergens in food products

Tree nut allergies are considered an important health issue in developed countries. To comply with the regulations on food labeling, reliable allergen detection methods are required. In this work we isolated almond-specific recombinant antibody fragments (scFv) from a commercial phage display library bypassing the use of live animals, hence being consistent with the latest policies on animal welfare. To this end an iterative selection procedure employing the Tomlinson I phage display library and a crude almond protein extract was carried out. Two different almond-specific scFv (named PD1F6 and PD2C9) were isolated after two rounds of biopanning, and an indirect phage ELISA was implemented to detect the presence of almond protein in foodstuffs. The isolated scFvs demonstrated to be highly specific and allowed detection of 40 ng mL?1 and 100 ng mL?1 of raw and roasted almond protein, respectively. The practical detection limit of the assay in almond spiked food products was 0.1 mg g?1 (110e120 ppm). The developed indirect phage ELISA was validated by analysis of 92 commercial food products, showing good correlation with the results obtained by a previously developed real-time PCR method for the detection of almond in foodstuffs. The selected phage clones can be affinity maturated to improve their sensitivity and genetically engineered to be employed in different assay formats.

Optimization of a label-free biosensor vertically characterized based on a periodic lattice of high aspect ratio SU-8 nano-pillars with a simplified 2D theoretical model

We have recently demonstrated a biosensor based on a lattice of SU8 pillars on a 1 μm SiO2/Si wafer by measuring vertically reflectivity as a function of wavelength. The biodetection has been proven with the combination of Bovine Serum Albumin (BSA) protein and its antibody (antiBSA). A BSA layer is attached to the pillars; the biorecognition of antiBSA involves a shift in the reflectivity curve, related with the concentration of antiBSA. A detection limit in the order of 2 ng/ml is achieved for a rhombic lattice of pillars with a lattice parameter (a) of 800 nm, a height (h) of 420 nm and a diameter(d) of 200 nm. These results correlate with calculations using 3D-finite difference time domain method. A 2D simplified model is proposed, consisting of a multilayer model where the pillars are turned into a 420 nm layer with an effective refractive index obtained by using Beam Propagation Method (BPM) algorithm. Results provided by this model are in good correlation with experimental data, reaching a reduction in time from one day to 15 minutes, giving a fast but accurate tool to optimize the design and maximizing sensitivity, and allows analyzing the influence of different variables (diameter, height and lattice parameter). Sensitivity is obtained for a variety of configurations, reaching a limit of detection under 1 ng/ml. Optimum design is not only chosen because of its sensitivity but also its feasibility, both from fabrication (limited by aspect ratio and proximity of the pillars) and fluidic point of view. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Biosensors based on vertically interrogated optofluidic sensing cells

El objetivo de la presente tesis doctoral es el desarrollo de un nuevo concepto de biosensor óptico sin marcado, basado en una combinación de técnicas de caracterización óptica de interrogación vertical y estructuras sub-micrométricas fabricadas sobre chips de silicio. Las características más importantes de dicho dispositivo son su simplicidad, tanto desde el punto de vista de medida óptica como de introducción de las muestras a medir en el área sensible, aspectos que suelen ser críticos en la mayoría de sensores encontrados en la literatura. Cada uno de los aspectos relacionados con el diseño de un biosensor, que son fundamentalmente cuatro (diseño fotónico, caracterización óptica, fabricación y fluídica/inmovilización química) son desarrollados en detalle en los capítulos correspondientes. En la primera parte de la tesis se hace una introducción al concepto de biosensor, en qué consiste, qué tipos hay y cuáles son los parámetros más comunes usados para cuantificar su comportamiento. Posteriormente se realiza un análisis del estado del arte en la materia, enfocado en particular en el área de biosensores ópticos sin marcado. Se introducen también cuáles son las reacciones bioquímicas a estudiar (inmunoensayos). En la segunda parte se describe en primer lugar cuáles son las técnicas ópticas empleadas en la caracterización: Reflectometría, Elipsometría y Espectrometría; además de los motivos que han llevado a su empleo. Posteriormente se introducen diversos diseños de las denominadas "celdas optofluídicas", que son los dispositivos en los que se va a producir la interacción bioquímica. Se presentan cuatro dispositivos diferentes, y junto con ellos, se proponen diversos métodos de cálculo teórico de la respuesta óptica esperada. Posteriormente se procede al cálculo de la sensibilidad esperada para cada una de las celdas, así como al análisis de los procesos de fabricación de cada una de ellas y su comportamiento fluídico. Una vez analizados todos los aspectos críticos del comportamiento del biosensor, se puede realizar un proceso de optimización de su diseño. Esto se realiza usando un modelo de cálculo simplificado (modelo 1.5-D) que permite la obtención de parámetros como la sensibilidad y el límite de detección de un gran número de dispositivos en un tiempo relativamente reducido. Para este proceso se escogen dos de las celdas optofluídicas propuestas. En la parte final de la tesis se muestran los resultados experimentales obtenidos. En primer lugar, se caracteriza una celda basada en agujeros sub-micrométricos como sensor de índice de refracción, usando para ello diferentes líquidos orgánicos; dichos resultados experimentales presentan una buena correlación con los cálculos teóricos previos, lo que permite validar el modelo conceptual presentado. Finalmente, se realiza un inmunoensayo químico sobre otra de las celdas propuestas (pilares nanométricos de polímero SU-8). Para ello se utiliza el inmunoensayo de albumina de suero bovino (BSA) y su anticuerpo (antiBSA). Se detalla el proceso de obtención de la celda, la funcionalización de la superficie con los bioreceptores (en este caso, BSA) y el proceso de biorreconocimiento. Este proceso permite dar una primera estimación de cuál es el límite de detección esperable para este tipo de sensores en un inmunoensayo estándar. En este caso, se alcanza un valor de 2.3 ng/mL, que es competitivo comparado con otros ensayos similares encontrados en la literatura. La principal conclusión de la tesis es que esta tipología de dispositivos puede ser usada como inmunosensor, y presenta ciertas ventajas respecto a los actualmente existentes. Estas ventajas vienen asociadas, de nuevo, a su simplicidad, tanto a la hora de medir ópticamente, como dentro del proceso de introducción de los bioanalitos en el área sensora (depositando simplemente una gota sobre la micro-nano-estructura). Los cálculos teorícos realizados en los procesos de optimización sugieren a su vez que el comportamiento del sensor, medido en magnitudes como límite de detección biológico puede ser ampliamente mejorado con una mayor compactación de pilares, alcanzandose un valor mínimo de 0.59 ng/mL). The objective of this thesis is to develop a new concept of optical label-free biosensor, based on a combination of vertical interrogation optical techniques and submicron structures fabricated over silicon chips. The most important features of this device are its simplicity, both from the point of view of optical measurement and regarding to the introduction of samples to be measured in the sensing area, which are often critical aspects in the majority of sensors found in the literature. Each of the aspects related to the design of biosensors, which are basically four (photonic design, optical characterization, fabrication and fluid / chemical immobilization) are developed in detail in the relevant chapters. The first part of the thesis consists of an introduction to the concept of biosensor: which elements consists of, existing types and the most common parameters used to quantify its behavior. Subsequently, an analysis of the state of the art in this area is presented, focusing in particular in the area of label free optical biosensors. What are also introduced to study biochemical reactions (immunoassays). The second part describes firstly the optical techniques used in the characterization: reflectometry, ellipsometry and spectrometry; in addition to the reasons that have led to their use. Subsequently several examples of the so-called "optofluidic cells" are introduced, which are the devices where the biochemical interactions take place. Four different devices are presented, and their optical response is calculated by using various methods. Then is exposed the calculation of the expected sensitivity for each of the cells, and the analysis of their fabrication processes and fluidic behavior at the sub-micrometric range. After analyzing all the critical aspects of the biosensor, it can be performed a process of optimization of a particular design. This is done using a simplified calculation model (1.5-D model calculation) that allows obtaining parameters such as sensitivity and the detection limit of a large number of devices in a relatively reduced time. For this process are chosen two different optofluidic cells, from the four previously proposed. The final part of the thesis is the exposition of the obtained experimental results. Firstly, a cell based sub-micrometric holes is characterized as refractive index sensor using different organic fluids, and such experimental results show a good correlation with previous theoretical calculations, allowing to validate the conceptual model presented. Finally, an immunoassay is performed on another typology of cell (SU-8 polymer pillars). This immunoassay uses bovine serum albumin (BSA) and its antibody (antiBSA). The processes for obtaining the cell surface functionalization with the bioreceptors (in this case, BSA) and the biorecognition (antiBSA) are detailed. This immunoassay can give a first estimation of which are the expected limit of detection values for this typology of sensors in a standard immunoassay. In this case, it reaches a value of 2.3 ng/mL, which is competitive with other similar assays found in the literature. The main conclusion of the thesis is that this type of device can be used as immunosensor, and has certain advantages over the existing ones. These advantages are associated again with its simplicity, by the simpler coupling of light and in the process of introduction of bioanalytes into the sensing areas (by depositing a droplet over the micro-nano-structure). Theoretical calculations made in optimizing processes suggest that the sensor Limit of detection can be greatly improved with higher compacting of the lattice of pillars, reaching a minimum value of 0.59 ng/mL).

Experimental comparison of FBARs and SMRs responsitivities to mass loadings

The utilisation of thin film technology to develop film bulk acoustic resonators (FBARs) and solidly mounted resonators (SMRs), offers great potential to outperform the sensitivity and minimum detection limit of gravimetric sensors. Up to now, the choice between FBARs and SMRs depends primarily on the users' ability to design and fabricate Bragg reflectors and/or membranes, because neither of these two types of resonators has been demonstrated to be superior to the other. In the work reported here, it is shown that identically designed FBARs and SMRs resonating at the same frequency exhibit different responsitivities, Rm, to mass loadings, being the FBARs more responsive than the SMRs. For the specific device design and resonant frequency (~2 GHz) of the resonators presented, FBARs' mass responsitivity is ~20% greater than that of SMRs, and although this value should not be taken as universal for all possible device designs, it clearly indicates that FBAR devices should be favoured over SMRs in gravimetric sensing applications.

Evaluation of the bioaccumulation kinetics of gold nanorods in vital mammalian organs by mean of TXRF spectrometry

This work presents the first application of total-reflection X-ray fluorescence (TXRF) spectrometry, a new and powerful alternative analytical method, to evaluation of the bioaccumulation kinetics of gold nanorods (GNRs) in various tissues upon intravenous administration in mice. The analytical parameters for developed methodology by TXRF were evaluated by means of the parallel analysis of bovine liver certified reference material samples (BCR-185R) doped with 10 μg/g gold. The average values (n = 5) achieved for gold measurements in lyophilized tissue weight were as follows: recovery 99.7%, expanded uncertainty (k = 2) 7%, repeatability 1.7%, detection limit 112 ng/g, and quantification limit 370 ng/g. The GNR bioaccumulation kinetics was analyzed in several vital mammalian organs such as liver, spleen, brain, and lung at different times. Additionally, urine samples were analyzed to study the kinetics of elimination of the GNRs by this excretion route. The main achievement was clearly differentiating two kinds of behaviors. GNRs were quickly bioaccumulated by highly vascular filtration organs such as liver and spleen, while GNRs do not show a bioaccumulation rates in brain and lung for the period of time investigated. In parallel, urine also shows a lack of GNR accumulation. TXRF has proven to be a powerful, versatile, and precise analytical technique for the evaluation of GNRs content in biological systems and, in a more general way, for any kind of metallic nanoparticles.

Propuesta metodológica para el análisis y protección de la calidad del agua subterránea de acuerdo con los requerimientos de la Directiva Marco y la Directiva derivada de Aguas Subterráneas

La protección de las aguas subterráneas es una prioridad de la política medioambiental de la UE. Por ello ha establecido un marco de prevención y control de la contaminación, que incluye provisiones para evaluar el estado químico de las aguas y reducir la presencia de contaminantes en ellas. Las herramientas fundamentales para el desarrollo de dichas políticas son la Directiva Marco del Agua y la Directiva Hija de Aguas Subterráneas. Según ellas, las aguas se consideran en buen estado químico si: • la concentración medida o prevista de nitratos no supera los 50 mg/l y la de ingredientes activos de plaguicidas, de sus metabolitos y de los productos de reacción no supera el 0,1 μg/l (0,5 μg/l para el total de los plaguicidas medidos) • la concentración de determinadas sustancias de riesgo es inferior al valor umbral fijado por los Estados miembros; se trata, como mínimo, del amonio, arsénico, cadmio, cloruro, plomo, mercurio, sulfatos, tricloroetileno y tetracloroetileno • la concentración de cualquier otro contaminante se ajusta a la definición de buen estado químico enunciada en el anexo V de la Directiva marco sobre la política de aguas • en caso de superarse el valor correspondiente a una norma de calidad o a un valor umbral, una investigación confirma, entre otros puntos, la falta de riesgo significativo para el medio ambiente. Analizar el comportamiento estadístico de los datos procedentes de la red de seguimiento y control puede resultar considerablemente complejo, debido al sesgo positivo que suelen presentar dichos datos y a su distribución asimétrica, debido a la existencia de valores anómalos y diferentes tipos de suelos y mezclas de contaminantes. Además, la distribución de determinados componentes en el agua subterránea puede presentar concentraciones por debajo del límite de detección o no ser estacionaria debida a la existencia de tendencias lineales o estacionales. En el primer caso es necesario realizar estimaciones de esos valores desconocidos, mediante procedimientos que varían en función del porcentaje de valores por debajo del límite de detección y el número de límites de detección aplicables. En el segundo caso es necesario eliminar las tendencias de forma previa a la realización de contrastes de hipótesis sobre los residuos. Con esta tesis se ha pretendido establecer las bases estadísticas para el análisis riguroso de los datos de las redes de calidad con objeto de realizar la evaluación del estado químico de las masas de agua subterránea para la determinación de tendencias al aumento en la concentración de contaminantes y para la detección de empeoramientos significativos, tanto en los casos que se ha fijado un estándar de calidad por el organismo medioambiental competente como en aquéllos que no ha sido así. Para diseñar una metodología que permita contemplar la variedad de casos existentes, se han analizado los datos de la Red Oficial de Seguimiento y Control del Estado Químico de las Aguas Subterráneas del Ministerio de Agricultura, Alimentación y Medio Ambiente (Magrama). A continuación, y dado que los Planes Hidrológicos de Cuenca son la herramienta básica de las Directivas, se ha seleccionado la Cuenca del Júcar, dada su designación como cuenca piloto en la estrategia de implementación común (CIS) de la Comisión Europea. El objetivo principal de los grupos de trabajo creados para ello se dirigió a implementar la Directiva Derivada de Agua Subterráneas y los elementos de la Directiva Marco del Agua relacionadas, en especial la toma de datos en los puntos de control y la preparación del primer Plan de Gestión de Cuencas Hidrográficas. Dada la extensión de la zona y con objeto de analizar una masa de agua subterránea (definida como la unidad de gestión en las Directivas), se ha seleccionado una zona piloto (Plana de Vinaroz Peñiscola) en la que se han aplicado los procedimientos desarrollados con objeto de determinar el estado químico de dicha masa. Los datos examinados no contienen en general valores de concentración de contaminantes asociados a fuentes puntuales, por lo que para la realización del estudio se han seleccionado valores de concentración de los datos más comunes, es decir, nitratos y cloruros. La estrategia diseñada combina el análisis de tendencias con la elaboración de intervalos de confianza cuando existe un estándar de calidad e intervalos de predicción cuando no existe o se ha superado dicho estándar. De forma análoga se ha procedido en el caso de los valores por debajo del límite de detección, tomando los valores disponibles en la zona piloto de la Plana de Sagunto y simulando diferentes grados de censura con objeto de comparar los resultados obtenidos con los intervalos producidos de los datos reales y verificar de esta forma la eficacia del método. El resultado final es una metodología general que integra los casos existentes y permite definir el estado químico de una masa de agua subterránea, verificar la existencia de impactos significativos en la calidad del agua subterránea y evaluar la efectividad de los planes de medidas adoptados en el marco del Plan Hidrológico de Cuenca. ABSTRACT Groundwater protection is a priority of the EU environmental policy. As a result, it has established a framework for prevention and control of pollution, which includes provisions for assessing the chemical status of waters and reducing the presence of contaminants in it. The measures include: • criteria for assessing the chemical status of groundwater bodies • criteria for identifying significant upward trends and sustained concentrations of contaminants and define starting points for reversal of such trends • preventing and limiting indirect discharges of pollutants as a result of percolation through soil or subsoil. The basic tools for the development of such policies are the Water Framework Directive and Groundwater Daughter Directive. According to them, the groundwater bodies are considered in good status if: • measured or predicted concentration of nitrate does not exceed 50 mg / l and the active ingredients of pesticides, their metabolites and reaction products do not exceed 0.1 mg / l (0.5 mg / l for total of pesticides measured) • the concentration of certain hazardous substances is below the threshold set by the Member States concerned, at least, of ammonium, arsenic, cadmium, chloride, lead, mercury, sulphates, trichloroethylene and tetrachlorethylene • the concentration of other contaminants fits the definition of good chemical status set out in Annex V of the Framework Directive on water policy • If the value corresponding to a quality standard or a threshold value is exceeded, an investigation confirms, among other things, the lack of significant risk to the environment. Analyzing the statistical behaviour of the data from the monitoring networks may be considerably complex due to the positive bias which often presents such information and its asymmetrical distribution, due to the existence of outliers and different soil types and mixtures of pollutants. Furthermore, the distribution of certain components in groundwater may have concentrations below the detection limit or may not be stationary due to the existence of linear or seasonal trends. In the first case it is necessary to estimate these unknown values, through procedures that vary according to the percentage of values below the limit of detection and the number of applicable limits of detection. In the second case removing trends is needed before conducting hypothesis tests on residuals. This PhD thesis has intended to establish the statistical basis for the rigorous analysis of data quality networks in order to conduct the evaluation of the chemical status of groundwater bodies for determining upward and sustained trends in pollutant concentrations and for the detection of significant deterioration in cases in which an environmental standard has been set by the relevant environmental agency and those that have not. Aiming to design a comprehensive methodology to include the whole range of cases, data from the Groundwater Official Monitoring and Control Network of the Ministry of Agriculture, Food and Environment (Magrama) have been analysed. Then, since River Basin Management Plans are the basic tool of the Directives, the Júcar river Basin has been selected. The main reason is its designation as a pilot basin in the common implementation strategy (CIS) of the European Commission. The main objective of the ad hoc working groups is to implement the Daughter Ground Water Directive and elements of the Water Framework Directive related to groundwater, especially the data collection at control stations and the preparation of the first River Basin Management Plan. Given the size of the area and in order to analyze a groundwater body (defined as the management unit in the Directives), Plana de Vinaroz Peñíscola has been selected as pilot area. Procedures developed to determine the chemical status of that body have been then applied. The data examined do not generally contain pollutant concentration values associated with point sources, so for the study concentration values of the most common data, i.e., nitrates and chlorides have been selected. The designed strategy combines trend analysis with the development of confidence intervals when there is a standard of quality and prediction intervals when there is not or the standard has been exceeded. Similarly we have proceeded in the case of values below the detection limit, taking the available values in Plana de Sagunto pilot area and simulating different degrees of censoring in order to compare the results obtained with the intervals achieved from the actual data and verify in this way the effectiveness of the method. The end result is a general methodology that integrates existing cases to define the chemical status of a groundwater body, verify the existence of significant impacts on groundwater quality and evaluate the effectiveness of the action plans adopted in the framework of the River Basin Management Plan.