Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.

Selectivity of diacylhydrazine insecticides to the predatory bug Orius laevigatus: In vivo and modeling/docking experiments

BACKGROUND: Knowledge of pesticide selectivity to natural enemies is necessary for a successful implementation of biological and chemical control methods in integrated pest management (IPM) programs. Diacylhydrazine (DAH)-based ecdysone agonists also known as molting-accelerating compounds (MACs) are considered a selective group of insecticides, and their compatibility with predatory Heteroptera, which are used as biological control agents, is known. However, their molecular mode of action has not been explored in beneficial insects such as Orius laevigatus (Fieber) (Hemiptera: Anthocoridae). RESULTS: In this project in vivo toxicity assays demonstrated that the DAH-based RH-5849, tebufenozide and methoxyfenozide have no toxic effect against O. laevigatus. The ligand-binding domain (LBD) of the ecdysone receptor (EcR) of O. laevigatus was sequenced and a homology protein model was constructed which confirmed a cavity structure with 12 ?-helixes, harboring the natural insect molting hormone 20-hydroxyecdysone. However, docking studies showed that a steric clash occurred for the DAH-based insecticides due to a restricted extent of the ligand-binding cavity of the EcR of O. laevigatus. CONCLUSIONS: The insect toxicity assays demonstrated that MACs are selective for O. laevigatus. The modeling/docking experiments are indications that these pesticides do not bind with the LBD-EcR of O. laevigatus and support that they show no biological effects in the predatory bug. These data help in explaining the compatible use of MACs together with predatory bugs in IPM programs. Keywords: Orius laevigatus, selectivity, diacylhydrazine insecticides, ecdysone receptor, homology modelling, docking studies.

Insect growth regulators as potential insecticides to control olive fruit fly (Bactrocera oleae Rossi): insect toxicity bioassays and molecular docking approach

Olive fruit fly, Bactrocera oleae (Rossi), is a key pest in olive orchards, causing serious economic damage. To date, the pest has already developed resistance to the insecticides commonly applied to control it. Thus, in searching for new products for an accurate resistance management programme, targeting the ecdysone receptor (EcR)might provide alternative compounds for use in such programmes. RESULTS: Residual contact and oral exposure in the laboratory of B. oleae adults to the dibenzoylhydrazine-based compounds methoxyfenozide, tebufenozide and RH-5849 showed different results. Methoxyfenozide and tebufenozide did not provoke anynegative effectsontheadults,but RH-5849 killed98-100%of the treated insects15 days after treatment. Theligand-binding domain (LBD) of the EcR of B. oleae (BoEcR-LBD) was sequenced, and a homology protein model was constructed. Owing to a restricted extent of the ligand-binding cavity of the BoEcR-LBD, docking experiments with the three tested insecticides showed a severe steric clash in the case of methoxyfenozide and tebufenozide, while this was not the case with RH-5849. CONCLUSION: IGR molecules similar to the RH-5849 molecule, and different from methoxyfenozide and tebufenozide, might have potential in controlling this pest.

Compatibilidad de Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) y Nesidiocoris tenuis (Reuter)(Hemiptera: Miridae), depredadores importantes en cultivos hortícolas protegidos, con nuevas barreras físicas selectivas y modernos plaguicidas

La nueva legislación en materia fitosanitaria se dirige hacia una Gestión Integrada de Plagas (GIP). Estos programas dan preferencia a aquellos métodos más respetuosos y sostenibles con el medio ambiente, siendo piezas claves en ellos el control biológico, el físico y otros de carácter no químico. Sin embargo, el uso de insecticidas selectivos es a veces necesario para el adecuado manejo de plagas en cultivos hortícolas. Por ello, el objetivo general de este estudio es aportar conocimientos para mejorar el control de plagas en cultivos hortícolas, mediante la integración de tres estrategias de lucha: biológica, física y química. Una parte de este trabajo ha consistido en el estudio de los posibles efectos que mallas tratadas con insecticida (bifentrin) pudieran provocar mediante diferentes ensayos de laboratorio, invernadero y campo, en los enemigos naturales Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) (depredador de trips), Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae) (depredador de mosca blanca y Tuta absoluta (Meirick) (Lepidoptera: Gelechiidae)), y otros agentes de biocontrol comúnmente usados en cultivos hortícolas protegidos. Este tipo de mallas se han empleado con éxito en entomología médica para controlar mosquitos vectores de la malaria, y actualmente se está trabajando en su desarrollo para uso agrícola como método de exclusión, y método directo de control de plagas. En los ensayos realizados en laboratorio, O. laevigatus y N. tenuis no fueron capaces de detectar la presencia de bifentrin en el ensayo de preferencia. Además, no se produjo mortalidad a corto plazo (72 horas) en ambos chinches depredadores. Por el contrario, se registró una elevada mortalidad cuando se expusieron por contacto a la malla tratada durante 72 horas en cajas de dimensiones reducidas (10 cm de diámetro X 3 cm de altura). En ensayos llevados a cabo bajo condiciones más reales de exposición, en un invernadero experimental con jaulas de 25 X 25 X 60 cm de altura, no se produjo ningún efecto en la mortalidad a corto plazo (72 horas) o en los parámetros reproductivos de O. laevigatus y N. tenuis. Finalmente, en ensayos de campo realizados en túneles semi-comerciales (8 m de largo X 6,5 m de ancho X 2,6 m de altura), ni las condiciones ambientales [temperatura, humedad relativa, radiación ultravioleta (UV) y fotosintéticamente activa (PAR)], ni los enemigos naturales, se vieron afectados por la presencia de la malla tratada con bifentrin en el cultivo. Sin embargo, los resultados no fueron concluyentes, debido al bajo establecimiento de los agentes de biocontrol liberados. Por lo tanto, más estudios son necesarios en invernaderos comerciales para confirmar los resultados preliminares de compatibilidad. Además, en este trabajo se han evaluado los efectos letales (mortalidad) y subletales (parámetros reproductivos) de seis modernos insecticidas sobre los chinches depredadores O. laevigatus y N. tenuis, mediante ensayos de laboratorio y persistencia. Los ensayos se realizaron por contacto residual, aplicando los insecticidas a la dosis máxima de campo sobre placas de cristal (laboratorio) o plantas (persistencia). Los productos fitosanitarios se seleccionaron por representar a un grupo de modernos plaguicidas con modos de acción en principio más selectivos para los enemigos naturales que antiguos plaguicidas como organoclorados, oroganofosforados o carbamatos, y por su uso frecuente en cultivos hortícolas donde O. laevigatus y N. tenuis están presentes. Todos ellos están incluidos o en proceso de inclusión en la lista comunitaria de sustancias activas para uso agrícola, Anexo I de la Directiva 91/414/CEE: abamectina y emamectina (avermectinas neurotóxicas, activadoras del canal del cloro), deltametrina (piretroide neurotóxico, modulador del canal del sodio, control positivo), flubendiamida (neurotóxico, modulador del receptor de rianodina), spinosad (naturalito neurotóxico, agonistas/antagonistas del receptor de nicotínico acetilcolina) y spiromesifen (inhibidor de la acetil CoA carboxilasa). El estudio mostró que O. laevigatus fue más susceptible a los insecticidas que N. tenuis. Además, los resultados revelaron que flubendiamida y spiromesifen fueron compatibles con los dos enemigos naturales estudiados, y por tanto se podrían usar en programas de GIP. Por el contrario, los insecticidas abamectina, deltametrina, emamectina y spinosad no fueron selectivos para ninguno de los chinches depredadores. Sin embargo, los estudios de persistencia demostraron que a pesar de que estos insecticidas no proporcionaron selectividad fisiológica, pueden proporcionar selectividad ecológica en algunos casos. Abamectina, deltametrina, emamectina y spinosad podrían ser compatibles con N. tenuis si el enemigo natural es introducido en el cultivo 4 días después de su aplicación. En el caso de O. laevigatus, abamectina, deltametrina y spinosad se clasificaron como persistentes, por lo tanto es necesario completar el estudio con experimentos de semi-campo y campo que determinen si es posible su uso conjunto en programas de GIP. Por otro lado, emamectina podría ser compatible con O. laevigatus si el enemigo natural es introducido en el cultivo 7 días después de su aplicación. Por último, se ha comprobado la selectividad de tres insecticidas aceleradores de la muda (MACs) (metoxifenocida, tebufenocida y RH-5849) sobre O. laevigatus y N. tenuis. Además de realizar estudios para evaluar la toxicidad en laboratorio de los insecticidas por contacto residual e ingestión (principal modo de acción de los MAC´s), se extrajo RNA de los insectos y con el cDNA obtenido se secuenció y clonó el dominio de unión al ligando (LBD) del receptor de ecdisona correspondiente a O. laevigatus (OlEcR-LBD) y N. tenuis (NtEcR-LBD). Posteriormente, se obtuvo la configuración en tres dimensiones del LBD y se estudió el acoplamiento de las moléculas de los tres insecticidas en la cavidad que forman las 12 α-hélices que constituyen el EcR-LBD. En el caso de N. tenuis se debe mencionar que no fue posible la obtención de la secuencia completa del LBD. Sin embargo, se obtuvo una secuencia parcial (hélice 6-hélice 11), que mostró una alta conservación de aminoácidos con respecto a la obtenida en O. laevigatus. Los ensayos de toxicidad mostraron que metoxifenocida, tebufenocida y RH-5849 no produjeron ningún efecto nocivo en ambos depredadores. Además, los estudios de modelado por homología y acoplamiento molecular llevados a cabo con O. laevigatus, también indicaron que los MACs no produjeron ningún efecto deletéreo en este enemigo natural. Por lo tanto, estos compuestos pueden ser aplicados de manera segura en programas de GIP en los cuales O. laevigatus y N. tenuis estén presentes. ABSTRACT The new pesticide legislation on pest control is aimed at integrated pest management (IPM). These programs are based on the most environmentally sustainable approaches, where biological, physical control and other non-chemical methods are the cornerstone. However, selective pesticides are often required for pest management on horticultural crops. Therefore, the main goal of this study is to provide knowledge to improve pest control on horticultural crops through the integration of three strategies: biological, physical and chemical. Firstly, the effects of insecticide treated nets (bifenthrin) were evaluated in different laboratory, greenhouse and field experiments on the natural enemies Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) (predator of thrips), Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae) (predator of whiteflies and Tuta absoluta (Meirick) (Lepidoptera: Gelechiidae)), and other biocontrol agents commonly used on protected horticultural crops. These types of nets have been successfully used in medical entomology to control mosquito malaria vectors, and work is currently being done on their use as exclusion barriers and as a direct method of pest control in agriculture. In experiments made under laboratory conditions, O. laevigatus and N. tenuis were not able to detect the presence of bifenthrin in a dual-choice test. Furthermore, no shortterm mortality (72 hours) was recorded on both predatory bugs. In contrast, a high mortality rate was found when they were exposed by contact to the bifenthrin-treated net for 72 hours in small cages (10 cm diameter X 3 cm high). In assays carried out under more realistic conditions of exposure, in an experimental greenhouse with cages of 25 X 25 X 60 cm high, short-term mortality (72 hours) and reproductive parameters were not affected. Lastly, in field experiments carried out in semi-commercial tunnels (8 m long X 6.5 m width X 2.6 m high), neither environmental conditions [temperature, relative humidity, ultraviolet (UV) and photosynthetically active radiation (PAR)] nor natural enemies were affected by the presence of the bifenthrin-treated net on the crop. However, results were not conclusive, mainly due to a low settlement of the released biocontrol agents, and further studies are needed in commercial greenhouses to confirm our preliminary results of compatibility. Secondly, the lethal (mortality) and sublethal effects (reproductive parameters) of six modern pesticides on the predatory bugs O. laevigatus and N. tenuis has been evaluated through laboratory and persistence experiments. Trials were carried out by residual contact, applying the insecticides to the maximum field recommended concentration on glass plates (laboratory) or plants (persistence). Insecticides were chosen as representatives of modern pesticides with a more selective mode of action on natural enemies than organochlorine, organophosphorus and carbamate insecticides. Moreover, they were also chosen because of their frequent use on horticultural crops where O. laevigatus and N. tenuis are present. All of them have been included or have been requested for inclusion in the community list of active substances on the agricultural market, Annex I of the European Directive 91/414/EEC: abamectin and emamectin (neurotoxic avermectins, chloride channel activators), deltamethrin (neutotoxic pyrethroid, sodium channel modulator, positive commercial standard), flubendiamide (neurotoxic, rianodine receptor modulator), spinosad (neurotoxic naturalyte, nicotinic acetylcholine receptor allosteric activator) and spiromesifen (inhibitors of acetyl CoA carboxylase). The study showed that O. laevigatus was more susceptible to all the studied pesticides than N. tenuis. In addition, the research results indicated no impact of flubendiamide and spiromesifen on the two natural enemies studied under laboratory conditions. Consequently, both pesticides are candidates to be included in IPM programmes where these biocontrol agents are present. On the other hand, abamectin, deltamethrin, emamectin and spinosad were not selective for both predatory bugs in laboratory experiments. However, persistence test demonstrated that in spite of the lack of physiological selectivity, these pesticides can provide ecological selectivity in some cases. Abamectin, deltamethrin, emamectin and spinosad could be compatible with N. tenuis if the mirid bug is released 4 days after the insecticide treatment on the crop. With regard to O. laevigatus, abamectin, deltamethrin and spinosad were classified as persistent in our assays, thus the study should be completed with semi-field and field experiments in order to ascertain their possible joint use in IPM programs. In contrast, emamectin could be compatible with O. laevigatus if the pirate bug is released 7 days after the insecticide treatment on the crop. Finally, the selectivity of three moulting accelerating compounds (MACs) (methoxyfenozide, tebufenozide and RH-5849) has also been evaluated on O. laevigatus and N. tenuis. In addition to laboratory experiments to evaluate the toxicity of the insecticides by residual contact and ingestion, molecular approaches were used as well. RNA of both insects was isolated, cDNA was subsequently synthesized and the complete sequence of the ligand binding domain (LBD) of the ecdysone receptor of O. laevigatus (OlEcR-LBD) and N. tenuis (NtEcR-LBD) were determined. Afterwards, the three dimensional structure of LBD was constructed. Finally, the docking of the insecticide molecules in the cavity delineated by the 12 α-helix that composed the EcRLBD was performed. In the case of N. tenuis, it should be noted that in spite of intensive efforts, we did not manage to complete the sequence for the LBD.However, a partial sequence of the LBD was obtained (helix 6-helix 11), and a strong conservation between the amino acids of N. tenuis and O. laevigatus was observed. Results showed no biological activity of methoxyfenozide, tebufenozide and RH-5849, on both predatory bugs. Moreover, modeling of the OlEcR-LBD and docking experiments also suggested that MACs were devoid of any deleterious effect on O. laevigatus. Therefore, our results indicate that these compounds could be safely applied in IPM programs in which O. laevigatus and N. tenuis are present.

Biometric authentication of users through iris by using key binding and similarity preserving hash functions = Autenticación biométrica de usuarios a través del iris mediante la ocultación de claves y funciones resumen que preservan la similitud

El extraordinario auge de las nuevas tecnologías de la información, el desarrollo de la Internet de las Cosas, el comercio electrónico, las redes sociales, la telefonía móvil y la computación y almacenamiento en la nube, han proporcionado grandes beneficios en todos los ámbitos de la sociedad. Junto a éstos, se presentan nuevos retos para la protección y privacidad de la información y su contenido, como la suplantación de personalidad y la pérdida de la confidencialidad e integridad de los documentos o las comunicaciones electrónicas. Este hecho puede verse agravado por la falta de una frontera clara que delimite el mundo personal del mundo laboral en cuanto al acceso de la información. En todos estos campos de la actividad personal y laboral, la Criptografía ha jugado un papel fundamental aportando las herramientas necesarias para garantizar la confidencialidad, integridad y disponibilidad tanto de la privacidad de los datos personales como de la información. Por otro lado, la Biometría ha propuesto y ofrecido diferentes técnicas con el fin de garantizar la autentificación de individuos a través del uso de determinadas características personales como las huellas dáctilares, el iris, la geometría de la mano, la voz, la forma de caminar, etc. Cada una de estas dos ciencias, Criptografía y Biometría, aportan soluciones a campos específicos de la protección de datos y autentificación de usuarios, que se verían enormemente potenciados si determinadas características de ambas ciencias se unieran con vistas a objetivos comunes. Por ello es imperativo intensificar la investigación en estos ámbitos combinando los algoritmos y primitivas matemáticas de la Criptografía con la Biometría para dar respuesta a la demanda creciente de nuevas soluciones más técnicas, seguras y fáciles de usar que potencien de modo simultáneo la protección de datos y la identificacíón de usuarios. En esta combinación el concepto de biometría cancelable ha supuesto una piedra angular en el proceso de autentificación e identificación de usuarios al proporcionar propiedades de revocación y cancelación a los ragos biométricos. La contribución de esta tesis se basa en el principal aspecto de la Biometría, es decir, la autentificación segura y eficiente de usuarios a través de sus rasgos biométricos, utilizando tres aproximaciones distintas: 1. Diseño de un esquema criptobiométrico borroso que implemente los principios de la biometría cancelable para identificar usuarios lidiando con los problemas acaecidos de la variabilidad intra e inter-usuarios. 2. Diseño de una nueva función hash que preserva la similitud (SPHF por sus siglas en inglés). Actualmente estas funciones se usan en el campo del análisis forense digital con el objetivo de buscar similitudes en el contenido de archivos distintos pero similares de modo que se pueda precisar hasta qué punto estos archivos pudieran ser considerados iguales. La función definida en este trabajo de investigación, además de mejorar los resultados de las principales funciones desarrolladas hasta el momento, intenta extender su uso a la comparación entre patrones de iris. 3. Desarrollando un nuevo mecanismo de comparación de patrones de iris que considera tales patrones como si fueran señales para compararlos posteriormente utilizando la transformada de Walsh-Hadarmard. Los resultados obtenidos son excelentes teniendo en cuenta los requerimientos de seguridad y privacidad mencionados anteriormente. Cada uno de los tres esquemas diseñados han sido implementados para poder realizar experimentos y probar su eficacia operativa en escenarios que simulan situaciones reales: El esquema criptobiométrico borroso y la función SPHF han sido implementados en lenguaje Java mientras que el proceso basado en la transformada de Walsh-Hadamard en Matlab. En los experimentos se ha utilizado una base de datos de imágenes de iris (CASIA) para simular una población de usuarios del sistema. En el caso particular de la función de SPHF, además se han realizado experimentos para comprobar su utilidad en el campo de análisis forense comparando archivos e imágenes con contenido similar y distinto. En este sentido, para cada uno de los esquemas se han calculado los ratios de falso negativo y falso positivo. ABSTRACT The extraordinary increase of new information technologies, the development of Internet of Things, the electronic commerce, the social networks, mobile or smart telephony and cloud computing and storage, have provided great benefits in all areas of society. Besides this fact, there are new challenges for the protection and privacy of information and its content, such as the loss of confidentiality and integrity of electronic documents and communications. This is exarcebated by the lack of a clear boundary between the personal world and the business world as their differences are becoming narrower. In both worlds, i.e the personal and the business one, Cryptography has played a key role by providing the necessary tools to ensure the confidentiality, integrity and availability both of the privacy of the personal data and information. On the other hand, Biometrics has offered and proposed different techniques with the aim to assure the authentication of individuals through their biometric traits, such as fingerprints, iris, hand geometry, voice, gait, etc. Each of these sciences, Cryptography and Biometrics, provides tools to specific problems of the data protection and user authentication, which would be widely strengthen if determined characteristics of both sciences would be combined in order to achieve common objectives. Therefore, it is imperative to intensify the research in this area by combining the basics mathematical algorithms and primitives of Cryptography with Biometrics to meet the growing demand for more secure and usability techniques which would improve the data protection and the user authentication. In this combination, the use of cancelable biometrics makes a cornerstone in the user authentication and identification process since it provides revocable or cancelation properties to the biometric traits. The contributions in this thesis involve the main aspect of Biometrics, i.e. the secure and efficient authentication of users through their biometric templates, considered from three different approaches. The first one is designing a fuzzy crypto-biometric scheme using the cancelable biometric principles to take advantage of the fuzziness of the biometric templates at the same time that it deals with the intra- and inter-user variability among users without compromising the biometric templates extracted from the legitimate users. The second one is designing a new Similarity Preserving Hash Function (SPHF), currently widely used in the Digital Forensics field to find similarities among different files to calculate their similarity level. The function designed in this research work, besides the fact of improving the results of the two main functions of this field currently in place, it tries to expand its use to the iris template comparison. Finally, the last approach of this thesis is developing a new mechanism of handling the iris templates, considering them as signals, to use the Walsh-Hadamard transform (complemented with three other algorithms) to compare them. The results obtained are excellent taking into account the security and privacy requirements mentioned previously. Every one of the three schemes designed have been implemented to test their operational efficacy in situations that simulate real scenarios: The fuzzy crypto-biometric scheme and the SPHF have been implemented in Java language, while the process based on the Walsh-Hadamard transform in Matlab. The experiments have been performed using a database of iris templates (CASIA-IrisV2) to simulate a user population. The case of the new SPHF designed is special since previous to be applied i to the Biometrics field, it has been also tested to determine its applicability in the Digital Forensic field comparing similar and dissimilar files and images. The ratios of efficiency and effectiveness regarding user authentication, i.e. False Non Match and False Match Rate, for the schemes designed have been calculated with different parameters and cases to analyse their behaviour.

Study of the influence of actin-binding proteins using linear analyses of cell deformability

The actin cytoskeleton plays a key role in the deformability of the cell and in mechanosensing. Here we analyze the contributions of three major actin cross-linking proteins, myosin II, a-actinin and filamin, to cell deformability, by using micropipette aspiration of Dictyostelium cells. We examine the applicability of three simple mechanical models: for small deformation, linear viscoelasticity and drop of liquid with a tense cortex; and for large deformation, a Newtonian viscous fluid. For these models, we have derived linearized equations and we provide a novel, straightforward methodology to analyze the experiments. This methodology allowed us to differentiate the effects of the cross-linking proteins in the different regimes of deformation. Our results confirm some previous observations and suggest important relations between the molecular characteristics of the actin-binding proteins and the cell behavior: the effect of myosin is explained in terms of the relation between the lifetime of the bond to actin and the resistive force; the presence of a-actinin obstructs the deformation of the cytoskeleton, presumably mainly due to the higher molecular stiffness and to the lower dissociation rate constants; and filamin contributes critically to the global connectivity of the network, possibly by rapidly turning over crosslinks during the remodeling of the cytoskeletal network, thanks to the higher rate constants, flexibility and larger size. The results suggest a sophisticated relationship between the expression levels of actinbinding proteins, deformability and mechanosensing.