683 resultados para Biosensor


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We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

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Polyelectrolyte multilayers (PEM) built by layer-by-layer technique have been extensively studied over the last years, resulting in a wide variety of current and potential applications. This technique can be used to construct thin films with different functionalities, or to functionalize surfaces with substantial different properties of those of the underlying substrates. The multilayering process is achieved by the alternate adsorption of oppositely charged polyelectrolytes. In this work we get advantage of the protein resistant property of the Poly (l-lysine)-graft-(polyethyleneglycol) to create protein patterns. Proteins can be immobilized on a surface by unspecific physical adsorption, covalent binding or through specific interactions. The first protein used in this work was laccase, a copper-containing redox enzyme that catalyse the oxidation of a broad range of polyphenols and aromatic substrates, coupled to the reduction of O2 to H2O without need of cofactors. Applications of laccases have been reported in food, pulp, paper, and textile industry, and also in biosensor development. Some uses require the immobilization of the enzyme on solid supports by adsorption, covalent attachment, entrapment, etc, on several substrates. Especially for biosensor development, highly active, stable and reproducible immobilization of laccase is required.

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Previous work of the research group [1-4] demonstrated the viability of using periodic lattices of micro and nanopillars, called Bio-photonic sensing Cells (BICELLs), as an optical biosensor vertically characterized by visible spectrometry. Also we have studied theoretically [5] the performance of the BICELLs by 2D and 3D simulation in orde r to optimize the biosensing response. In this work we present the fabrication and biosensing comparison of different geometrical parameters on periodic lattices of pillars in order to discuss theoretical conclusions with these results. In this way, we have explored the biosensing response of other patter ns such as crosses, stars, cylinders, concentrical cylinders (Figure 1). Also we introduced a novel method to test the BICELLs in a cost-effective way by using an ultra-thin film of SU-8 spin-coated onto the patterns to reproduce the effect of a biofilm attached to the biosensor surface. Finally we have tested the biosensing response of the different geometries by the well-known Bovine Serum Albumin (BSA) immunoassay and compared with the theoretical simulation.

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The analysis of the interference modes has an increasing application, especially in the field of optical biosensors. In this type of sensors, the displacement Δν of the interference modes of the transduction signal is observed when a particular biological agent is placed over the biosensor. In order to measure this displacement, the position of a maximum (or a minimum) of the signal must be detected before and after placing the agent over the sensor. A parameter of great importance for this kind of sensors is the period Pν of the signal, which is inversely proportional to the optical thickness h0 of the sensor in the absence of the biological agent. The increase of this period improves the sensitivity of the sensor but it worsens the detection of the maximum. In this paper, authors analyze the propagation of uncertainties in these sensors when using least squares techniques for the detection of the maxima (or minima) of the signal. Techniques described in supplement 2 of the ISO-GUM Guide are used. The result of the analysis allows a metrological educated answer to the question of which is the optimal period Pν of the signal. El análisis del comportamiento de los modos de interferencia tiene una aplicación cada vez más amplia, especialmente en el campo de los biosensores ópticos. En este tipo de sensores se observa el desplazamiento Δν de los modos de interferencia de la señal de transducción al reconocer un de-terminado agente biológico. Para medir ese desplazamiento se debe detectar la posición de un máximo o mínimo de la señal antes y después de dicho desplazamiento. En este tipo de biosensores un parámetro de gran importancia es el periodo Pν de la señal el cual es inversamente proporcional al espesor óptico h0 del sensor en ausencia de agente biológico. El aumento de dicho periodo mejora la sensibilidad del sensor pero parece dificultar la detección del mínimo o máximo. Por tanto, su efecto sobre la incertidumbre del resultado de la medida presenta dos efectos contrapuestos: la mejora de la sensibilidad frente a la dificultad creciente en la detección del mínimo ó máximo. En este trabajo, los autores analizan la propagación de incertidumbres en estos sensores utilizando herramientas de ajuste por MM.CC. para la detección de los mínimos o máximos de la señal y técnicas de propagación de incertidumbres descritas en el suplemento 2 de la Guía ISO-GUM. El resultado del análisis permite dar una respuesta, justificada desde el punto de vista metrológico, de en que condiciones es conveniente o no aumentar el periodo Pν de la señal.

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El gran crecimiento de los sistemas MEMS (Micro Electro Mechanical Systems) así como su presencia en la mayoría de los dispositivos que usamos diariamente despertó nuestro interés. Paralelamente, la tecnología CMOS (Complementary Metal Oxide Semiconductor) es la tecnología más utilizada para la fabricación de circuitos integrados. Además de ventajas relacionadas con el funcionamiento electrónico del dispositivo final, la integración de sistemas MEMS en la tecnología CMOS reduce significantemente los costes de fabricación. Algunos de los dispositivos MEMS con mayor variedad de aplicaciones son los microflejes. Estos dispositivos pueden ser utilizados para la extracción de energía, en microscopios de fuerza atómica o en sensores, como por ejemplo, para biodetección. Los materiales piezoeléctricos más comúnmente utilizados en aplicaciones MEMS se sintetizan a altas temperaturas y por lo tanto no son compatibles con la tecnología CMOS. En nuestro caso hemos usado nitruro de alumino (AlN), que se deposita a temperatura ambiente y es compatible con la tecnología CMOS. Además, es biocompatible, y por tanto podría formar parte de un dispositivo que actúe como biosensor. A lo largo de esta tesis hemos prestado especial atención en desarrollar un proceso de fabricación rápido, reproducible y de bajo coste. Para ello, todos los pasos de fabricación han sido minuciosamente optimizados. Los parámetros de sputtering para depositar el AlN, las distintas técnicas y recetas de ataque, los materiales que actúan como electrodos o las capas sacrificiales para liberar los flejes son algunos de los factores clave estudiados en este trabajo. Una vez que la fabricación de los microflejes de AlN ha sido optimizada, fueron medidos para caracterizar sus propiedades piezoeléctricas y finalmente verificar positivamente su viabilidad como dispositivos piezoeléctricos. ABSTRACT The huge growth of MEMS (Micro Electro Mechanical Systems) as well as their presence in most of our daily used devices aroused our interest on them. At the same time, CMOS (Complementary Metal Oxide Semiconductor) technology is the most popular technology for integrated circuits. In addition to advantages related with the electronics operation of the final device, the integration of MEMS with CMOS technology reduces the manufacturing costs significantly. Some of the MEMS devices with a wider variety of applications are the microcantilevers. These devices can be used for energy harvesting, in an atomic force microscopes or as sensors, as for example, for biodetection. Most of the piezoelectric materials used for these MEMS applications are synthesized at high temperature and consequently are not compatible with CMOS technology. In our case we have used aluminum nitride (AlN), which is deposited at room temperature and hence fully compatible with CMOS technology. Otherwise, it is biocompatible and and can be used to compose a biosensing device. During this thesis work we have specially focused our attention in developing a high throughput, reproducible and low cost fabrication process. All the manufacturing process steps of have been thoroughly optimized in order to achieve this goal. Sputtering parameters to synthesize AlN, different techniques and etching recipes, electrode material and sacrificial layers are some of the key factors studied in this work to develop the manufacturing process. Once the AlN microcantilevers fabrication was optimized, they were measured to characterize their piezoelectric properties and to successfully check their viability as piezoelectric devices.

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El objetivo de esta tesis es el desarrollo y caracterización de biosensores ópticos sin marcado basados en celdas sensoras biofotónicas (BICELLs). Éstas son un nuevo concepto de biosensor desarrollado por el grupo de investigación y consiste en la combinación de técnicas de interrogación vertical, junto a estructuras fotónicas producidas usando métodos de micro- y nanofabricación. Varias conclusiones son extraídas de este trabajo. La primera, que se ha definido una BICELL estándar basada en interferómetros Fabry-Perot (FP). Se ha demostrado su capacidad para la comparación de rendimiento entre BICELLs estructuradas y para la realización de inmunoensayos de bajo coste. Se han estudiado diferentes técnicas de fabricación disponibles para la producción de BICELLs. Se determinó que la litografía de contacto a nivel de oblea produce estructuras de bajo coste, reproducibles y de alta calidad. La resolución alcanzada ha sido de 700 nm. El estudio de la respuesta a inmunoensayos de las BICELLs producidas se ha desarrollado en este trabajo. Se estudió la influencia de BICELLs basadas en diferentes geometrías y tamaños. De aquí resulta un nuevo enfoque para predecir el comportamiento de respuesta para la detección biológica de cualquier biosensor óptico estructurado, relacionando su superficie efectiva y su sensibilidad óptica. También se demostró una técnica novedosa y de bajo coste para la caracterización experimental de la sensibilidad óptica, basada en el depósito de películas ultradelgadas. Finalmente, se ha demostrado el uso de BICELLs desarrolladas en esta tesis, en la detección de aplicaciones reales, tales como hormonas, virus y proteínas. ABSTRACT The objective of this thesis is the development and characterization of optical label-free biosensors based on Bio-Photonic sensing Cells (BICELLs). BICELL is a novel biosensor concept developed by the research group, and it consists of a combination of vertical interrogation optical techniques and photonic structures produced by using micro- and nano-fabrication methods. Several main conclusions are extracted from this work. Firstly, a standard BICELL is defined based on FP interferometers, which demonstrated its capacity for accomplishing performance comparisons among different structured BICELLs, as well as to achieve low-cost immunoassays. Different available fabrication techniques were studied for BICELL manufacturing. It is found that contact lithography at wafer scale produce cost-effective, reproducible and high quality structures. The resolution achieved was 700 nm. Study on the response of developed BICELLs to immunoassays is performed within this work. It is therefore studied the influence of BICELLs based on different geometries and sizes in the immunoassay, which resulted in a new approach to predict the biosensing behaviour of any structured optical biosensor relating to its effective surface and optical sensitivity. Also, it is demonstrated a novel and low-cost characterization technique of the experimental optical sensitivity, based on ultrathin-film deposition. Finally, it is also demonstrated the capability of using the developed BICELLs in this thesis for real applications detection of hormones, virus and proteins.

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El núcleo fundamental de esta tesis doctoral es un modelo teórico de la interacción de la luz con un tipo particular de biosensor óptico. Este biosensor se compone de dos regiones: en la región inferior puede haber capas de materiales con diferentes espesores y propiedades ópticas, apiladas horizontalmente; en la zona superior, sobre la que incide directamente el haz de luz, puede haber estructuras que hacen que las propiedades ópticas cambien tanto en el plano horizontal como en la dirección vertical. Estos biosensores responden ópticamente de forma diferente al ser iluminados dependiendo de que su superficie externa esté, en mayor o menor medida, recubierta con diferentes tipos de material biológico. En esta tesis se define un modelo analítico aproximado que permite simular la respuesta óptica de biosensores con estructuras en su región más externa. Una vez comprobada la validez práctica del modelo mediante comparación con medidas experimentales, éste se utiliza en el diseño de biosensores de rendimiento óptimo y en la definición de nuevas técnicas de interrogación óptica. En particular, el sistema de transducción IROP (Increased Relative Optical Power), basado en el efecto que produce la presencia de material biológico, en la potencia total reflejada por la celda biosensora en determinados intervalos espectrales, es uno de los sistemas que ha sido patentado y es objeto de desarrollo por la empresa de base tecnológica BIOD [www.biod.es/], estando ya disponibles en este momento varios dispositivos de diagnóstico basados en esta idea. Los dispositivos basados en este sistema de transducción han demostrado su eficiencia en la detección de proteínas y agentes infecciosos como los rotavirus y el virus del dengue. Finalmente, el modelo teórico desarrollado se utiliza para caracterizar las propiedades ópticas de algunos de los materiales de los que se fabrican los biosensores, así como las de las capas de material biológico formadas en las diferentes fases de un inmunoensayo. Los parámetros ópticos de las capas mencionadas se obtienen mediante el método general de ajuste por mínimos cuadrados a las curvas experimentales obtenidas en los inmunoensayos. ABSTRACT The core of this thesis is the theoretical modeling of the interaction of light with a particular type of optical biosensor. This biosensor consists of two parts: in the lower region may have layers of materials with different thicknesses and optical properties, stacked horizontally; at the top, on which directly affects the light beam, there may be structures that make optical properties change in both, the horizontal and in the vertical direction. These biosensors optically respond differently when illuminated depending on its external surface is greater or lesser extent, coated with different types of biological material. In this thesis an approximate analytical model to simulate the optical response of biosensors with structures in its outer region is defined. After verifying the practical validity of the model by comparison with experimental measurements, it is used in the design of biosensors with optimal performance and the definition of new optical interrogation techniques. In particular, the transduction system IROP (Increased Relative Optical Power) based on the effect of the presence of biological material in the total power reflected from the biosensor cell in certain spectral ranges, has been patented and is under development by the startup company BIOD [www.biod.es/], being already available at this time, several diagnostic devices based on this idea. Devices based on this transduction system have proven their efficiency in detecting proteins and infectious agents such as rotavirus and virus of dengue. Finally, the developed theoretical model is used to characterize the optical properties of some of the materials from which biosensors are fabricated, as well as the optical properties of the biological material layers formed at different stages of an immunoassay. The optical parameters of the layers above are obtained by the general method of least squares fit to the experimental curves obtained in immunoassays.

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Anti-P antibodies present in sera from patients with chronic Chagas heart disease (cChHD) recognize peptide R13, EEEDDDMGFGLFD, which encompasses the C-terminal region of the Trypanosoma cruzi ribosomal P1 and P2 proteins. This peptide shares homology with the C-terminal region (peptide H13 EESDDDMGFGLFD) of the human ribosomal P proteins, which is in turn the target of anti-P autoantibodies in systemic lupus erythematosus (SLE), and with the acidic epitope, AESDE, of the second extracellular loop of the β1-adrenergic receptor. Anti-P antibodies from chagasic patients showed a marked preference for recombinant parasite ribosomal P proteins and peptides, whereas anti-P autoantibodies from SLE reacted with human and parasite ribosomal P proteins and peptides to the same extent. A semi-quantitative estimation of the binding of cChHD anti-P antibodies to R13 and H13 using biosensor technology indicated that the average affinity constant was about 5 times higher for R13 than for H13. Competitive enzyme immunoassays demonstrated that cChHD anti-P antibodies bind to the acidic portions of peptide H13, as well as to peptide H26R, encompassing the second extracellular loop of the β1 adrenoreceptor. Anti-P antibodies isolated from cChHD patients exert a positive chronotropic effect in vitro on cardiomyocytes from neonatal rats, which resembles closely that of anti-β1 receptor antibodies isolated from the same patient. In contrast, SLE anti-P autoantibodies have no functional effect. Our results suggest that the adrenergic-stimulating activity of anti-P antibodies may be implicated in the induction of functional myocardial impairments observed in cChHD.

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Recruitment of intracellular proteins to the plasma membrane is a commonly found requirement for the initiation of signal transduction events. The recently discovered pleckstrin homology (PH) domain, a structurally conserved element found in ∼100 signaling proteins, has been implicated in this function, because some PH domains have been described to be involved in plasma membrane association. Furthermore, several PH domains bind to the phosphoinositides phosphatidylinositol-(4,5)-bisphosphate and phosphatidylinositol-(3,4,5)-trisphosphate in vitro, however, mostly with low affinity. It is unclear how such weak interactions can be responsible for observed membrane binding in vivo as well as the resulting biological phenomena. Here, we investigate the structural and functional requirements for membrane association of cytohesin-1, a recently discovered regulatory protein of T cell adhesion. We demonstrate that both the PH domain and the adjacent carboxyl-terminal polybasic sequence of cytohesin-1 (c domain) are necessary for plasma membrane association and biological function, namely interference with Jurkat cell adhesion to intercellular adhesion molecule 1. Biosensor measurements revealed that phosphatidylinositol-(3,4,5)-trisphosphate binds to the PH domain and c domain together with high affinity (100 nM), whereas the isolated PH domain has a substantially lower affinity (2–3 μM). The cooperativity of both elements appears specific, because a chimeric protein, consisting of the c domain of cytohesin-1 and the PH domain of the β-adrenergic receptor kinase does not associate with membranes, nor does it inhibit adhesion. Moreover, replacement of the c domain of cytohesin-1 with a palmitoylation–isoprenylation motif partially restored the biological function, but the specific targeting to the plasma membrane was not retained. Thus we conclude that two elements of cytohesin-1, the PH domain and the c domain, are required and sufficient for membrane association. This appears to be a common mechanism for plasma membrane targeting of PH domains, because we observed a similar functional cooperativity of the PH domain of Bruton’s tyrosine kinase with the adjacent Bruton’s tyrosine kinase motif, a novel zinc-containing fold.

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Binding properties of lignin peroxidase (LiP) from the basidiomycete Phanerochaete chrysosporium against a synthetic lignin (dehydrogenated polymerizate, DHP) were studied with a resonant mirror biosensor. Among several ligninolytic enzymes, only LiP specifically binds to DHP. Kinetic analysis revealed that the binding was reversible, and that the dissociation equilibrium constant was 330 μM. The LiP–DHP interaction was controlled by the ionization group with a pKa of 5.3, strongly suggesting that a specific amino acid residue plays a role in lignin binding. A one-electron transfer from DHP to oxidized intermediates LiP compounds I and II (LiPI and LiPII) was characterized by using a stopped-flow technique, showing that binding interactions of DHP with LiPI and LiPII led to saturation kinetics. The dissociation equilibrium constants for LiPI–DHP and LiPII–DHP interactions were calculated to be 350 and 250 μM, and the first-order rate constants for electron transfer from DHP to LiPI and to LiPII were calculated to be 46 and 16 s−1, respectively. These kinetic and spectral studies strongly suggest that LiP is capable of oxidizing lignin directly at the protein surface by a long-range electron transfer process. A close look at the crystal structure suggested that LiP possesses His-239 as a possible lignin-binding site on the surface, which is linked to Asp-238. This Asp residue is hydrogen-bonded to the proximal His-176. This His–Asp⋅⋅⋅proximal-His motif would be a possible electron transfer route to oxidize polymeric lignin.

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We recently derived a CD4-independent virus from HIV-1/IIIB, termed IIIBx, which interacts directly with the chemokine receptor CXCR4 to infect cells. To address the underlying mechanism, a cloned Env from the IIIBx swarm (8x) was used to produce soluble gp120. 8x gp120 bound directly to cells expressing only CXCR4, whereas binding of IIIB gp120 required soluble CD4. Using an optical biosensor, we found that CD4-induced (CD4i) epitopes recognized by mAbs 17b and 48d were more exposed on 8x than on IIIB gp120. The ability of 8x gp120 to bind directly to CXCR4 and to react with mAbs 17b and 48d in the absence of CD4 indicated that this gp120 exists in a partially triggered but stable state in which the conserved coreceptor-binding site in gp120, which overlaps with the 17b epitope, is exposed. Substitution of the 8x V3 loop with that from the R5 virus strain BaL resulted in an Env (8x-V3BaL) that mediated CD4-independent CCR5-dependent virus infection and a gp120 that bound to CCR5 in the absence of CD4. Thus, in a partially triggered Env protein, the V3 loop can change the specificity of coreceptor use but does not alter CD4 independence, indicating that these properties are dissociable. Finally, IIIBx was more sensitive to neutralization by HIV-positive human sera, a variety of anti-IIIB gp120 rabbit sera, and CD4i mAbs than was IIIB. The sensitivity of this virus to neutralization and the stable exposure of a highly conserved region of gp120 suggest new strategies for the development of antibodies and small molecule inhibitors to this functionally important domain.

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The performance of an amperometric biosensor, consisting of a subcutaneously implanted miniature (0.29 mm diameter, 5 × 10−4 cm2 mass transporting area), 90 s 10–90% rise/decay time glucose electrode, and an on-the-skin electrocardiogram Ag/AgCl electrode was tested in an unconstrained, naturally diabetic, brittle, type I, insulin-dependent chimpanzee. The chimpanzee was trained to wear on her wrist a small electronic package and to present her heel for capillary blood samples. In five sets of measurements, averaging 5 h each, 82 capillary blood samples were assayed, their concentrations ranging from 35 to 400 mg/dl. The current readings were translated to blood glucose concentration by assaying, at t = 1 h, one blood sample for each implanted sensor. The rms error in the correlation between the sensor-measured glucose concentration and that in capillary blood was 17.2%, 4.9% above the intrinsic 12.3% rms error of the Accu-Chek II reference, through which the illness of the chimpanzee was routinely managed. Linear regression analysis of the data points taken at t>1 h yielded the relationship (Accu-Chek) = 0.98 × (implanted sensor) + 4.2 mg/dl, r2 = 0.94. The capillary blood and the subcutaneous glucose concentrations were statistically indistinguishable when the rate of change was less than 1 mg/(dl⋅min). However, when the rate of decline exceeded 1.8 mg/(dl⋅min) after insulin injection, the subcutaneous glucose concentration was transiently higher.

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Cassette mutagenesis was used to identify side chains in human interleukin 5 (hIL-5) that mediate binding to hIL-5 receptor alpha chain (hIL-5R alpha). A series of single alanine substitutions was introduced into a stretch of residues in the C-terminal region, including helix D, which previously had been implicated in receptor alpha chain recognition and which is aligned on the IL-5 surface so as to allow the topography of receptor binding residues to be examined. hIL-5 and single site mutants were expressed in COS cells, their interactions with hIL-5R alpha were measured by a sandwich surface plasmon resonance biosensor method, and their biological activities were measured by an IL-5-dependent cell proliferation assay. A pattern of mutagenesis effects was observed, with greatest impact near the interface between the two four-helix bundles of IL-5, in particular at residues Glu-110 and Trp-111, and least at the distal ends of the D helices. This pattern suggests the possibility that residues near the interface of the two four-helix bundles in hIL-5 comprise a central patch or hot spot, which constitutes an energetically important alpha chain recognition site. This hypothesis suggests a structural explanation for the 1:1 stoichiometry observed for the complex of hIL-5 with hIL-5R alpha.

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The neonatal Fc receptor (FcRn) transports maternal IgG from ingested milk in the gut to the bloodstream of newborn mammals. An FcRn dimer was observed in crystals of the receptor alone and of an FcRn-Fc complex, but its biological relevance was unknown. Here we use surface plasmon resonance-based biosensor assays to assess the role of FcRn dimerization in IgG binding. We find high-affinity IgG binding when FcRn is immobilized on a biosensor chip in an orientation facilitating dimerization but not when its orientation disrupts dimerization. This result supports a model in which IgG-induced dimerization of FcRn is relevant for signaling the cell to initiate endocytosis of the IgG-FcRn complex.

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Este trabalho descreve a preparação e caracterização de eletrodos modificados com azul da Prússia e materiais relacionados e a sua aplicação na construção de biossensores enzimáticos amperométricos para a detecção de oxalato e de glicose. Os materiais utilizados na modificação dos eletrodos foram azul da Prússia e compostos híbridos formados por hexacianoferrato de níquel e polipirrol ou hexacianoferrato de cobre e polipirrol. Os materiais lubridos mostraram-se capazes de mediar na eletroredução de peróxido de hidrogênio, mesmo em eletrólitos contendo Na+, apresentando melhor desempenho analítico quando comparados aos respectivos hexacianoferratos sem a presença do polímero condutor. Estes materiais foram utilizados com êxito na construção de biossensores para oxalato e para glicose, imobilizando as enzimas Oxalato Oxidase e Glicose Oxidase, respectivamente. Também foi estudada a preparação de um biossensor para a detecção de glicose utilizando a técnica de automontagem eletrostática camada por camada. Esta técnica permite otimizar o processo de immobilização da enzima, obtendo excelente desempenho analítico com pouca quantidade de enzima. Finalmente, são apresentadas a síntese, caracterização e aplicação de nanopartículas de azul da Prússia na determinação de peróxido de hidrogênio. Foi possível preparar nanopartículas com um diâmetro médio de 5 nm, as quais foram imobilizadas em eletrodos mediante a técnica de automontagem eletrostática camada por camada, a fim de estudar seu comportamento eletroquímico.