Control of a Nonlinear Teleoperation System by State Convergence

In this work, we proposes a control strategy that allows the remote manipulator follow the local manipulator through the state convergence even if it has a delay in the communication channel. The bilateral control of the teleoperator system considers the case were the human operator applies a constant force on the local manipulator and when the interaction of the remote manipulator with the environment is considered passive. The stability analysis was performed using Lyapunov- Krasovskii functional, it showed for the case with constant delay, that using a proposed control algorithm by state convergence resulted in asymptotically stable, local and remote the nonlinear teleoperation system.

Advances in Control of Teleoperation System by State Convergence

In this work, we proposes a control strategy by state convergence applied to bilateral control of a nonlinear teleoperator system with constant delay. The bilateral control of the teleoperator system considers the case when the human operator applies a constant force on the local manipulator and when the interaction of the remote manipulator with the environment is considered passive. The stability analysis is performed using Lyapunov-Krasovskii functional, it showed that using an control algorithm by state convergence for the case with constant delay, the nonlinear local and remote teleoperation system is asymptotically stable, also speeds converge to zero and position tracking is achieved. This work also presents the implementation of an experimental platform. The mechanical structure of the arm that is located in the remote side has been built and the electric servomechanism has been mounted to control their movement.

Evolutionary computation of forests with Degree- and Role-Constrained Minimum Spanning Trees

Finding the degree-constrained minimum spanning tree (DCMST) of a graph is a widely studied NP-hard problem. One of its most important applications is network design. Here we deal with a new variant of the DCMST problem, which consists of finding not only the degree- but also the role-constrained minimum spanning tree (DRCMST), i.e., we add constraints to restrict the role of the nodes in the tree to root, intermediate or leaf node. Furthermore, we do not limit the number of root nodes to one, thereby, generally, building a forest of DRCMSTs. The modeling of network design problems can benefit from the possibility of generating more than one tree and determining the role of the nodes in the network. We propose a novel permutation-based representation to encode these forests. In this new representation, one permutation simultaneously encodes all the trees to be built. We simulate a wide variety of DRCMST problems which we optimize using eight different evolutionary computation algorithms encoding individuals of the population using the proposed representation. The algorithms we use are: estimation of distribution algorithm, generational genetic algorithm, steady-state genetic algorithm, covariance matrix adaptation evolution strategy, differential evolution, elitist evolution strategy, non-elitist evolution strategy and particle swarm optimization. The best results are for the estimation of distribution algorithms and both types of genetic algorithms, although the genetic algorithms are significantly faster.

UAS See-and-Avoid Strategy using a Fuzzy Logic Controller Optimized by Cross-Entropy in Scaling Factors and Membership Functions.

This work aims to develop a novel Cross-Entropy (CE) optimization-based fuzzy controller for Unmanned Aerial Monocular Vision-IMU System (UAMVIS) to solve the seeand-avoid problem using its accurate autonomous localization information. The function of this fuzzy controller is regulating the heading of this system to avoid the obstacle, e.g. wall. In the Matlab Simulink-based training stages, the Scaling Factor (SF) is adjusted according to the specified task firstly, and then the Membership Function (MF) is tuned based on the optimized Scaling Factor to further improve the collison avoidance performance. After obtained the optimal SF and MF, 64% of rules has been reduced (from 125 rules to 45 rules), and a large number of real flight tests with a quadcopter have been done. The experimental results show that this approach precisely navigates the system to avoid the obstacle. To our best knowledge, this is the first work to present the optimized fuzzy controller for UAMVIS using Cross-Entropy method in Scaling Factors and Membership Functions optimization.

Self-adaptive strategy based on fuzzy control systems for improving performance in wireless sensors networks

The solutions to cope with new challenges that societies have to face nowadays involve providing smarter daily systems. To achieve this, technology has to evolve and leverage physical systems automatic interactions, with less human intervention. Technological paradigms like Internet of Things (IoT) and Cyber-Physical Systems (CPS) are providing reference models, architectures, approaches and tools that are to support cross-domain solutions. Thus, CPS based solutions will be applied in different application domains like e-Health, Smart Grid, Smart Transportation and so on, to assure the expected response from a complex system that relies on the smooth interaction and cooperation of diverse networked physical systems. The Wireless Sensors Networks (WSN) are a well-known wireless technology that are part of large CPS. The WSN aims at monitoring a physical system, object, (e.g., the environmental condition of a cargo container), and relaying data to the targeted processing element. The WSN communication reliability, as well as a restrained energy consumption, are expected features in a WSN. This paper shows the results obtained in a real WSN deployment, based on SunSPOT nodes, which carries out a fuzzy based control strategy to improve energy consumption while keeping communication reliability and computational resources usage among boundaries.

Análisis de la cadena de valor, canales cortos de comercialización y horticultura multifuncional como opciones de puesta en valor: Caso de la Huerta de Aranjuez

La Vega de Aranjuez ha sido desde hace siglos conocida por la notoriedad de sus jardines y huertas históricas y también, en épocas más recientes, por ser la despensa de Madrid. A mediados del siglo XX, sin embargo, con las transformaciones que el sector agrario ha experimentado no sólo a nivel local, sino a escala global, empezó un proceso de declive que se ha acentuado en los últimos años. Paralelamente, en el año 2001, la Unesco declara el Paisaje Cultural de Aranjuez, como Patrimonio de la Humanidad con un valor universal excepcional. Parte de lo que sustenta este reconocimiento a nivel internacional radica en las peculiaridades del paisaje que conforma la actividad agraria. El cambio de orientación, eminentemente hortofrutícola hacia cultivos extensivos y superficies en barbecho, y la pérdida de importancia del sector, no han pasado desapercibidos para la administración local y han sido varios los intentos de recuperación y dinamización del sector en los últimos años. La investigación de la que es objeto esta Tesis Doctoral surgió por iniciativa del Ayuntamiento de Aranjuez, que en al año 2010 deseó conocer la situación del sector hortícola en el municipio, para lo cual, encargó un estudio a la UPM-ETSIA. Para conocer la realidad desde una perspectiva integral, se planteó abordar el análisis desde la perspectiva de Cadena de Valor. Las implicaciones de este concepto, su evolución y su papel como instrumento de análisis de la cadena alimentaria, han sido revisadas y presentadas en el epígrafe del Marco Conceptual. Por cadena de valor se entiende el conjunto de procesos desde el consumidor, a través de los proveedores que proporcionan productos, servicios e información que añaden valor hacia los clientes (Lambert & Cooper, 2000; Chen, 2004). Para el análisis de la situación del sector hortícola en Aranjuez, se procedió en varios pasos, los cuales constituyeron la primera fase de la investigación y contemplaron lo siguiente: 1. La identificación de los problemas y de las demandas de los actores de la cadena, realizando cortes transversales en el mercado a distintos niveles para conocer los puntos de vista de los operadores de la cadena (Gunasekaran & Patel ,2004; Rojas, 2009; Schiefer, 2007). Para ello se diseñaron cuestionarios y se dirigieron a representantes de cinco eslabones de la cadena presentes en el caso de estudio: Agricultores (15), Mayoristas (11), Detallistas (55), Consumidores (85) y Restaurantes (36), tanto en Aranjuez como en Madrid (un total de 202). 2. Análisis D.A.F.O de cada uno de los eslabones y de la cadena completa, como herramienta para identificar y sintetizar la problemática y las potencialidades del sector. 3. Análisis global de la Cadena de Valor mediante el Método de Organización Sectorial, según Briz, de Felipe y Briz (2010), el cual permite estudiar aspectos de la estructura, la conducta y el funcionamiento de la cadena. 4. Jornada de análisis por parte de un Panel de Expertos en la sede de la Fundación Foro Agrario, en la cual se presentaron las conclusiones del análisis de la cadena de valor y se plantearon estrategias para la dinamización del sector. Con los resultados del análisis en esta primera fase de la investigación, se obtuvo una panorámica de la cadena de valor. Algunos de los aspectos más destacados son los siguientes: • El eslabón productivo en Aranjuez está muy atomizado y trabaja por lo general de forma independiente. Cultiva hasta veinte productos hortícolas diferentes, entre los cuales los frutales están casi en desaparición y hay poca presencia de producto ecológico. Le preocupan los precios poco estables y bajos y por lo general no trabaja con contratos. •El eslabón mayorista prácticamente carece de presencia en Aranjuez y está representado en su mayoría por operadores de Mercamadrid, los cuales demandan mayores volúmenes y mejor normalización de los productos hortícolas procedentes de Aranjuez. • El eslabón detallista consultado es diverso (con representación de comercios minoristas, supermercados e hipermercados) y también demanda mayores volúmenes de producción y mejoras en la normalización. Un 80% conoce los productos de Aranjuez, especialmente el espárrago y la fresa-fresón citados en un 74% y 63% de los casos respectivamente. • En el eslabón de consumidores, el 79% de los encuestados da importancia a la procedencia de los productos hortícolas y un 82% conoce los productos de la Huerta de Aranjuez, siendo los más consumidos el espárrago y el fresón. Un 42% de los encuestados compra producto ecológico por razones de salud, sabor y buscando la ausencia de químicos. • El eslabón de restaurantes es un gran consumidor de hortalizas, la gran mayoría de los productos incluidos en el análisis se oferta en más del 75% de los casos. Las más presentes son tomate y espárrago. La fresa y el fresón (en un 83% de los casos), y el espárrago (72%) seguido de la alcachofa (44%) son los productos de Aranjuez que más se conocen en el conjunto de los restaurantes entrevistados. El 75% de los restaurantes prefiere el producto fresco frente al procesado o congelado. La mayoría de los restaurantes locales (92%) estaría dispuesto a incluir en su carta una diferenciación para los productos de Aranjuez. Sin embargo, en el resto de restaurantes el porcentaje es mucho menor (21%). Entre las conclusiones del análisis se evidenció que un 52% de las ventas de los agricultores se realizaba sin intermediarios y un 69% de los consumidores se manifestaba interesado en adquirir productos de Aranjuez directamente del campo a su casa. Se identificó de esta manera que el acortamiento de la cadena se está utilizando como una forma de crear valor. Para profundizar en este aspecto, se planteó una segunda fase en la investigación. Además de estudiar diversos aspectos de los canales cortos de comercialización, se planteó estudiar el enfoque multifuncional de la horticultura, como estrategia para poner en valor la Huerta ribereña. Para dar una coherencia con la fase anterior, el planteamiento se realizó también desde la perspectiva de la cadena de valor, orientando la consulta hacia el eslabón consumidor. De esta manera, se realizó una consulta mediante cuestionario a 221 consumidores sobre diferentes aspectos relativos a los Canales Cortos de Comercialización (CCC) y la Horticultura Multifuncional (HM)1, lo cual permitió realizar un análisis cuantitativo de diferentes variables. Para completar la visión integral de la cadena corta, se seleccionaron 6 proyectos significativos que son ejemplos de diversas tipologías de canales cortos de comercialización en Aranjuez y Madrid, como representantes del denominado eslabón de “Promotores de CCC” y se consultó también a la Asociación de Productores de la Huerta de Aranjuez, constituida formalmente en el año 2014, como representante del eslabón Productor. Para la obtención de información, la cual tiene un carácter cualitativo en el caso de estos dos eslabones de la cadena, se realizaron cuestionarios y Estudios de Caso de cada proyecto. Los cuestionarios de esta segunda fase de consulta a los eslabones de la cadena corta contuvieron cuestiones relativas a los canales cortos de comercialización, tanto a nivel general (concepto de canal corto, puntos fuertes y ventajas que aportan, dificultades para su desarrollo, factores clave para su éxito) como para el caso concreto de la Huerta de Aranjuez (perfil del consumidor, factores implicados en la compra de verduras, utilización de diversas modalidades de canal corto, relación con las tecnologías de la información y comunicación (TICs) y la producción ecológica o la importancia del factor confianza). También aspectos relacionados con la Horticultura Multifuncional, como son, la valoración de diferentes actividades o proyectos de carácter agro-turístico, educativo, social o terapéutico, o la percepción del consumidor de las actividades de huerta como fuente de bienestar y como agente satisfactor de diversas necesidades humanas. Para completar la visión sobre estos dos temas, CCC y HM, se realizó una consulta mediante cuestionario a Expertos en el campo de los canales cortos de comercialización, procedentes del ámbito académico, y a Profesionales en activo trabajando en proyectos de horticultura social y terapéutica. La información aportada, aunque tiene carácter cualitativo, complementa el estudio ofreciendo la perspectiva académica en el caso de los canales cortos y amplía la información sobre la horticultura multifuncional, tratando cuestiones relativas al desempeño profesional o a la formación existente en España en el campo de la horticultura social y terapéutica. Los resultados de esta segunda fase de la investigación, entre otras cuestiones, evidenciaron que: • Los canales cortos de comercialización implican mucho más que la simple reducción de intermediarios y comprenden una gran diversidad de tipologías. • Los casos estudiados, están enfocados en su mayoría al producto ecológico y su funcionamiento está muy fundamentado en el uso de TICs y en el factor confianza. • En relación a la compra de verduras en el ámbito de los canales cortos, son aspectos muy valorados por el consumidor la calidad del producto, la rapidez y frescura con la que llega del campo a la mesa y que el Producto sea recogido en su punto óptimo de maduración. • Las actividades en el ámbito de la horticultura multifuncional son valoradas positivamente por los consumidores, siendo las más puntuadas las de huerto educativo, huerto terapéutico, seguidas de visitas guiadas y degustaciones de productos de huerta en restaurantes. • Por lo general existe una valoración muy alta de la huerta como fuente de bienestar y de satisfacción de necesidades humanas básicas, especialmente las de una alimentación saludable y de conexión con la naturaleza. Para terminar esta síntesis de la investigación realizada, se presentan las principales conclusiones a nivel global de la Tesis, que son las siguientes: 1. La metodología de cadena de valor ha resultado adecuada para conocer la complejidad y el funcionamiento del sector hortícola arancetano desde una perspectiva integral. 2. La Huerta de Aranjuez cuenta con importantes fortalezas, sustentadas en la calidad de sus suelos y en la fama que mantienen sus productos, pero también debilidades. Esto supone poco volumen de producción, que dificulta la relación con mayoristas y grandes detallistas. 3. El acortamiento de la cadena, mediante canales cortos de comercialización se ha identificado como una forma de creación de valor en la cadena. Existen oportunidades de abastecimiento a consumidores de Madrid mediante canales cortos, sin embargo, las modalidades que requieren mayor organización o requisitos de producción ecológica todavía no están desarrolladas. 4. La producción ecológica podría ser una estrategia para crear valor pero todavía es un método de cultivo muy minoritario en la cadena productiva arancetana. 5. Las peculiaridades de la Huerta de Aranjuez propician la puesta en práctica del enfoque multifuncional de la horticultura como vía de desarrollo económico. Los resultados apuntan a una posible demanda de servicios que contemplen actividades de horticultura de carácter educativo, terapéutico y agro-turístico, conducidas por profesionales. Existe una percepción positiva sobre el potencial de la huerta como fuente de bienestar y de satisfacción de necesidades humanas básicas. 6. La puesta en marcha de proyectos empresariales en el ámbito de la horticultura social es una apuesta interesante para crear valor en la huerta que ha sido valorada positivamente por los eslabones de la cadena corta consultados. 7. El campo de la Horticultura Multifuncional que contempla aspectos educativos, sociales y terapéuticos conforma una disciplina con posibilidades de desarrollo que en la investigación se perciben como limitadas por la falta de profesionales y su acceso a una formación adecuada en España. El estudio de los Canales Cortos de Comercialización y de la Horticultura Multifuncional como vías de puesta en valor en el caso de la Huerta de Aranjuez ha tenido un carácter exploratorio y en gran parte cualitativo en esta Tesis Doctoral. Ambos conceptos han desvelado cierta complejidad y requieren de un mayor conocimiento en diversos aspectos para su puesta en práctica con éxito. Se abre, por tanto, un campo para futuras investigaciones que profundicen en estos ámbitos. ABSTRACT La Vega de Aranjuez has been known for centuries for the reputation of its orchards and historic gardens and, more recently, as the pantry of Madrid. However, in the mid-twentieth century, with the transformations in agriculture, not only locally, but globally, began a process of decline that has been accentuated in recent years. Meanwhile, in 2001, Unesco declared Aranjuez Cultural Landscape, as a World Heritage Site with outstanding universal value. Part of what underpins this international recognition lies in the peculiarities of the landscape created by farming. The shift, from an eminently horticultural vocation to extensive field crops and fallow surfaces, and the loss of importance of the sector, have not gone unnoticed for local authorities and have been several attempts at recovery and revitalization of the sector in recent years. The beginning of this research came at the initiative of the municipality of Aranjuez, which in 2010 wanted to know the situation of the horticultural sector, for which he commissioned a study by the UPM-ETSIA. To know reality from an integral perspective, it was proposed to approach the analysis from the perspective of value chain. The implications of this concept, its evolution and its role as an instrument of analysis of the food chain, have been reviewed and presented in Chapter 3.2. The value chain concept refers to all the processes from the consumer, through suppliers who provide products, services and information that add value to customers (Lambert & Cooper, 2000; Chen, 2004). For the analysis of the situation of the horticultural sector in Aranjuez, which constituted the first phase of research, it proceeded in several steps: 1. Identifying the problems and demands of the actors in the chain, making transverse cuts in the market at different levels to meet the views of the chain operators (Gunasekaran & Patel , 2004; Rojas, 2009; Schiefer, 2007). Questionnaires were designed for it and went to representatives of the five links in the chain: Farmers (15), Wholesalers (11), Retailers (55), Consumers (85) and Restaurants (36), both in Aranjuez and Madrid (a total of 202). 2. SWOT analysis of each chain actor and of the whole supply chain, as a tool to identify and synthesize the problems and potential of the sector. 3. Analysis of the whole supply chain by Industrial Organization Method according to Briz et al. (2010), which allows to study aspects of the structure, conduct and performance of the chain. 4. Analysis by a Panel of Experts at Foro Agrario Foundation headquarters, where the conclusions of the analysis were presented and strategies for the revitalization of the sector were raised. The results of the analysis in this first phase of the research, presented an overview of the value chain. Some of the highlights are: - The productive sector in Aranjuez is very fragmented and usually works independently. With a wide variety of horticultural products (up to 20), fruit crops almost disappearing and little presence of organic product. Is concerned about the unstable and low prices and usually does not work with contracts. - The wholesale sector with virtually no presence in Aranjuez is represented mostly by Mercamadrid operators, who demand higher volumes and better standardization of horticultural products from Aranjuez. - The retailer sector is diversified (with representation from retailers, supermarkets and hypermarkets) and also demand higher production volumes and improved standardization. 80% know the products of Aranjuez, especially asparagus and strawberry-strawberry cited by 74% and 63% of cases respectively. - Among the consumers, 79% give importance to the origin of horticultural products and 82% know the products from Aranjuez, the most consumed asparagus and strawberries. 42% buy organic products for health, taste and absence of chemicals. - Restaurants are big consumers of vegetables, most of the products included in the analysis is offered in over 75% of cases. The most: tomato and asparagus. Strawberry (83% of cases), and asparagus (72%) followed by the artichoke (44%) are the products of Aranjuez more known in all the surveyed restaurants. 75% of the restaurants prefer fresh product against processed or frozen. Most local restaurants (92%) would be willing to include in their menu a differentiation for products of Aranjuez. However, for those restaurants from Madrid the percentage is much lower (21%). Among the conclusions of the analysis it showed that 52% of sales were realized from farmers without intermediaries and 69% of consumers expressed interest in acquiring products directly from field to table. It has been identified that the shortening of the chain is being used as a way to create value. To deepen this aspect, a second phase investigation arose. Besides studying various aspects of the short supply chains, it was also proposed to study the functional approach of horticulture as a strategy to add value. To provide consistency with the previous phase, the focus was also conducted from the perspective of the value chain, directing the query to consumers. Thus, again it was used the questionnaire as a methodological tool, and 221 consumers were asked about different aspects of the Short Suppy Chains (SSC) and Multifunctional Horticulture (MH)2, which allowed a quantitative analysis of several variables. To complete the comprehensive view of the short chain, 6 significant projects were selected as examples of different types of short supply chains in Aranjuez and Madrid, representing "SSC Promoters" and also the “Asociación de Productores de la Huerta de Aranjuez”, formally constituted in 2014, was asked representing the productive sector. The Study Case and again the questionnaire were elected as methodological tools in a qualitative analysis. The questionnaires of this second phase of research contained short supply chain issues, as a general topic (short supply chain concept, strengths and advantages they bring difficulties for its development, key factors success) and also refered to the case of Aranjuez (consumer profile, factors involved in the purchase of vegetables, use of several types of short supply chains, relation with information and communication technologies (ICTs) and organic production or the importance of trust in short supply chains). It also contemplated aspects of multifunctional horticulture, such as the valuation of different activities (agro-tourism, educational, social or therapeutic horticulture) and consumer perception about horticultural activities as a source of welfare and satisfactor of human needs. To complete the vision of these two issues, SSC and MH, experts in the field of short supply chains and professionals working in the field of social and therapeutic horticulture were asked. The qualitative information provided, complements the study offering a new perspective in the value chain analysis, such as those relating to job performance, the difficulties encountered or training existing in our country in the field of social and therapeutic horticulture. The results of this second phase of research showed that: Short supply chains involve much more than simply reducing intermediaries and cover a wide range of types. The cases studied are mostly focused on ecological product and its operation is heavily based on the use of ICTs and the trust factor. In connection with the purchase of vegetables in the field of short supply chains, product quality, speed and freshness with which comes from the field to the table and products picked at its peak maturation, are aspects highly valued by the consumer. Activities in the field of multifunctional horticulture are positively valued by consumers, the most scored: the educational garden, therapeutic garden, followed by guided tours and tastings of vegetables from Aranjuez in restaurants. Horticultural activities were highly valuated as a source of welfare and satisfaction of human needs, especially those of healthy eating and connection with nature. To complete this summary, the main conclusions of the research are presented as follows: 1. The value chain approach has been adequate to meet the complexity and operation of the horticultural sector in Aranjuez from a holistic perspective. 2. La Huerta de Aranjuez has important strengths, underpinned by the quality of its soils and fame that keep their products, but also weaknesses. This implies low volume of production, which makes difficult the link with wholesalers and large retailers. 3. The shortening of the chain by short supply chains has been identified as a way of creating value in the chain. Opportunities exist to supply consumers from Madrid by short supply chains, however, methods that require greater organization or requirements of organic production are not yet developed. 4. Organic production could be a strategy to create value but is not generally being implemented in the production chain. 5. The peculiarity of the Huerta de Aranjuez favours the implementation of the multifunctional approach as a means of economic development. The results point to a possible demand for multifunctional horticulture that include educational, therapeutic and agro-tourism activities. There is a positive perception of the potential of horticultural activities as a source of welfare and satisfaction of basic human needs. 6. The implementation of business projects in the field of social horticulture are an interesting way to create value that has been highly valued in the short supply chain. 7. The field of Multifunctional Horticulture which includes educational, social and therapeutic aspects, forms a discipline with possibilities of development, which in research are seen as limited by the lack of professionals and access to adequate training in our country. The study of Short Supply Chains and Multifunctional Horticulture as strategies to create value in the case of the Huerta de Aranjuez has an exploratory character and largely qualitative in this research. Both concepts have revealed some complexity and require greater knowledge in various aspects for successful implementation. It opens therefore a field for future research to deepen in these areas.

Design Parameter Analysis of Point Absorber WEC via an Evolutionary-Algorithm-Based Dimensioning Tool

Wave energy conversion has an essential difference from other renewable energies since the dependence between the devices design and the energy resource is stronger. Dimensioning is therefore considered a key stage when a design project of Wave Energy Converters (WEC) is undertaken. Location, WEC concept, Power Take-Off (PTO) type, control strategy and hydrodynamic resonance considerations are some of the critical aspects to take into account to achieve a good performance. The paper proposes an automatic dimensioning methodology to be accomplished at the initial design project stages and the following elements are described to carry out the study: an optimization design algorithm, its objective functions and restrictions, a PTO model, as well as a procedure to evaluate the WEC energy production. After that, a parametric analysis is included considering different combinations of the key parameters previously introduced. A variety of study cases are analysed from the point of view of energy production for different design-parameters and all of them are compared with a reference case. Finally, a discussion is presented based on the results obtained, and some recommendations to face the WEC design stage are given.

Peptide design by artificial neural networks and computer-based evolutionary search

A technique for systematic peptide variation by a combination of rational and evolutionary approaches is presented. The design scheme consists of five consecutive steps: (i) identification of a “seed peptide” with a desired activity, (ii) generation of variants selected from a physicochemical space around the seed peptide, (iii) synthesis and testing of this biased library, (iv) modeling of a quantitative sequence-activity relationship by an artificial neural network, and (v) de novo design by a computer-based evolutionary search in sequence space using the trained neural network as the fitness function. This strategy was successfully applied to the identification of novel peptides that fully prevent the positive chronotropic effect of anti-β1-adrenoreceptor autoantibodies from the serum of patients with dilated cardiomyopathy. The seed peptide, comprising 10 residues, was derived by epitope mapping from an extracellular loop of human β1-adrenoreceptor. A set of 90 peptides was synthesized and tested to provide training data for neural network development. De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity.

A structural view of evolutionary divergence

Two directed evolution experiments on p-nitrobenzyl esterase yielded one enzyme with a 100-fold increased activity in aqueous-organic solvents and another with a 17°C increase in thermostability. Structures of the wild type and its organophilic and thermophilic counterparts are presented at resolutions of 1.5 Å, 1.6 Å, and 2.0 Å, respectively. These structures identify groups of interacting mutations and demonstrate how directed evolution can traverse complex fitness landscapes. Early-generation mutations stabilize flexible loops not visible in the wild-type structure and set the stage for further beneficial mutations in later generations. The mutations exert their influence on the esterase structure over large distances, in a manner that would be difficult to predict. The loops with the largest structural changes generally are not the sites of mutations. Similarly, none of the seven amino acid substitutions in the organophile are in the active site, even though the enzyme experiences significant changes in the organization of this site. In addition to reduction of surface loop flexibility, thermostability in the evolved esterase results from altered core packing, helix stabilization, and the acquisition of surface salt bridges, in agreement with other comparative studies of mesophilic and thermophilic enzymes. Crystallographic analysis of the wild type and its evolved counterparts reveals networks of mutations that collectively reorganize the active site. Interestingly, the changes that led to diversity within the α/β hydrolase enzyme family and the reorganization seen in this study result from main-chain movements.

Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII

Two RNases H of mammalian tissues have been described: RNase HI, the activity of which was found to rise during DNA replication, and RNase HII, which may be involved in transcription. RNase HI is the major mammalian enzyme representing around 85% of the total RNase H activity in the cell. By using highly purified calf thymus RNase HI we identified the sequences of several tryptic peptides. This information enabled us to determine the sequence of the cDNA coding for the large subunit of human RNase HI. The corresponding ORF of 897 nt defines a polypeptide of relative molecular mass of 33,367, which is in agreement with the molecular mass obtained earlier by SDS/PAGE. Expression of the cloned ORF in Escherichia coli leads to a polypeptide, which is specifically recognized by an antiserum raised against calf thymus RNase HI. Interestingly, the deduced amino acid sequence of this subunit of human RNase HI displays significant homology to RNase HII from E. coli, an enzyme of unknown function and previously judged as a minor activity. This finding suggests an evolutionary link between the mammalian RNases HI and the prokaryotic RNases HII. The idea of a mammalian RNase HI large subunit being a strongly conserved protein is substantiated by the existence of homologous ORFs in the genomes of other eukaryotes and of all eubacteria and archaebacteria that have been completely sequenced.

A single response mechanism is responsible for evolutionary adaptive variation in a bird’s laying date

Many proximate factors determine a bird’s laying date, including environmental and social stimuli as well as individual responses to internal and external factors. However, the relative importance of these factors has not been experimentally demonstrated. Here we show that (i) large differences in the onset of first clutches between different populations result from variation in different responses to photoperiod and not from variation in responses to any other proximate factors and (ii) the same response mechanism causes maladaptive laying dates in habitats modified by humans. We present, to our knowledge, the first experimental demonstration that a single response mechanism is responsible for evolutionary adaptive intraspecific variation in a vertebrate life history trait.

A Novel Fluorescence-based Genetic Strategy Identifies Mutants of Saccharomyces cerevisiae Defective for Nuclear Pore Complex Assembly

Nuclear pore complexes (NPCs) are large proteinaceous portals for exchanging macromolecules between the nucleus and the cytoplasm. Revealing how this transport apparatus is assembled will be critical for understanding the nuclear transport mechanism. To address this issue and to identify factors that regulate NPC formation and dynamics, a novel fluorescence-based strategy was used. This approach is based on the functional tagging of NPC proteins with the green fluorescent protein (GFP), and the hypothesis that NPC assembly mutants will have distinct GFP-NPC signals as compared with wild-type (wt) cells. By fluorescence-activated cell sorting for cells with low GFP signal from a population of mutagenized cells expressing GFP-Nup49p, three complementation groups were identified: two correspond to mutant nup120 and gle2 alleles that result in clusters of NPCs. Interestingly, a third group was a novel temperature-sensitive allele of nup57. The lowered GFP-Nup49p incorporation in the nup57-E17 cells resulted in a decreased fluorescence level, which was due in part to a sharply diminished interaction between the carboxy-terminal truncated nup57pE17 and wt Nup49p. Interestingly, the nup57-E17 mutant also affected the incorporation of a specific subset of other nucleoporins into the NPC. Decreased levels of NPC-associated Nsp1p and Nup116p were observed. In contrast, the localizations of Nic96p, Nup82p, Nup159p, Nup145p, and Pom152p were not markedly diminished. Coincidentally, nuclear import capacity was inhibited. Taken together, the identification of such mutants with specific perturbations of NPC structure validates this fluorescence-based strategy as a powerful approach for providing insight into the mechanism of NPC biogenesis.

Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels

The function of many of the uncharacterized open reading frames discovered by genomic sequencing can be determined at the level of expressed gene products, the proteome. However, identifying the cognate gene from minute amounts of protein has been one of the major problems in molecular biology. Using yeast as an example, we demonstrate here that mass spectrometric protein identification is a general solution to this problem given a completely sequenced genome. As a first screen, our strategy uses automated laser desorption ionization mass spectrometry of the peptide mixtures produced by in-gel tryptic digestion of a protein. Up to 90% of proteins are identified by searching sequence data bases by lists of peptide masses obtained with high accuracy. The remaining proteins are identified by partially sequencing several peptides of the unseparated mixture by nanoelectrospray tandem mass spectrometry followed by data base searching with multiple peptide sequence tags. In blind trials, the method led to unambiguous identification in all cases. In the largest individual protein identification project to date, a total of 150 gel spots—many of them at subpicomole amounts—were successfully analyzed, greatly enlarging a yeast two-dimensional gel data base. More than 32 proteins were novel and matched to previously uncharacterized open reading frames in the yeast genome. This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.

Characterization of avian T-cell receptor γ genes

In birds and mammals T cells develop along two discrete pathways characterized by expression of either the αβ or the γδ T-cell antigen receptors (TCRs). To gain further insight into the evolutionary significance of the γδ T-cell lineage, the present studies sought to define the chicken TCRγ locus. A splenic cDNA library was screened with two polymerase chain reaction products obtained from genomic DNA using primers for highly conserved regions of TCR and immunoglobulin genes. This strategy yielded cDNA clones with characteristics of mammalian TCR γ chains, including canonical residues considered important for proper folding and stability. Northern blot analysis with the TCRγ cDNA probe revealed 1.9-kb transcripts in the thymus, spleen, and a γδ T-cell line, but not in B or αβ T-cell lines. Three multimember Vγ subfamilies, three Jγ gene segments, and a single constant region Cγ gene were identified in the avian TCRγ locus. Members of each of the three Vγ subfamilies were found to undergo rearrangement in parallel during the first wave of thymocyte development. TCRγ repertoire diversification was initiated on embryonic day 10 by an apparently random pattern of V-Jγ recombination, nuclease activity, and P- and N-nucleotide additions to generate a diverse repertoire of avian TCRγ genes early in ontogeny.

Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage

We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage φC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, φflu, in the Haemophilus influenzae genome, and two small prophage-like elements, φRv1 and φRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.