Reference list of sources used for two experimental data files dataBSRN and dataMixed

Increasing amounts of data is collected in most areas of research and application. The degree to which this data can be accessed, analyzed, and retrieved, is a decisive in obtaining progress in fields such as scientific research or industrial production. We present a novel methodology supporting content-based retrieval and exploratory search in repositories of multivariate research data. In particular, our methods are able to describe two-dimensional functional dependencies in research data, e.g. the relationship between ination and unemployment in economics. Our basic idea is to use feature vectors based on the goodness-of-fit of a set of regression models to describe the data mathematically. We denote this approach Regressional Features and use it for content-based search and, since our approach motivates an intuitive definition of interestingness, for exploring the most interesting data. We apply our method on considerable real-world research datasets, showing the usefulness of our approach for user-centered access to research data in a Digital Library system.

Multi-agent location system in wireless networks

In this paper we propose a flexible Multi-Agent Architecture together with a methodology for indoor location which allows us to locate any mobile station (MS) such as a Laptop, Smartphone, Tablet or a robotic system in an indoor environment using wireless technology. Our technology is complementary to the GPS location finder as it allows us to locate a mobile system in a specific room on a specific floor using the Wi-Fi networks. The idea is that any MS will have an agent known at a Fuzzy Location Software Agent (FLSA) with a minimum capacity processing at its disposal which collects the power received at different Access Points distributed around the floor and establish its location on a plan of the floor of the building. In order to do so it will have to communicate with the Fuzzy Location Manager Software Agent (FLMSA). The FLMSAs are local agents that form part of the management infrastructure of the Wi-Fi network of the Organization. The FLMSA implements a location estimation methodology divided into three phases (measurement, calibration and estimation) for locating mobile stations (MS). Our solution is a fingerprint-based positioning system that overcomes the problem of the relative effect of doors and walls on signal strength and is independent of the network device manufacturer. In the measurement phase, our system collects received signal strength indicator (RSSI) measurements from multiple access points. In the calibration phase, our system uses these measurements in a normalization process to create a radio map, a database of RSS patterns. Unlike traditional radio map-based methods, our methodology normalizes RSS measurements collected at different locations on a floor. In the third phase, we use Fuzzy Controllers to locate an MS on the plan of the floor of a building. Experimental results demonstrate the accuracy of the proposed method. From these results it is clear that the system is highly likely to be able to locate an MS in a room or adjacent room.

Explotación de servicios de la Infraestructura de Datos Espaciales de España (IDEE) en dispositivos móviles

En los últimos años el número de dispositivos móviles y smartphones ha aumentado drásticamente, así como el número de aplicaciones destinadas a estos. Los desarrolladores siempre se han visto frenados en la creación de estas aplicaciones debido a la complejidad que supone la diversidad de sistemas operativos (Android, iOS, Windows Phone, etc), que utilizan lenguajes de programación diferentes, haciendo que, para poder desarrollar una aplicación que funcione en estas plataformas, en verdad haya que implementar una aplicación independiente para cada una de las plataformas. Para solucionar este problema han surgido frameworks, como Appcelerator Titanium, que permiten escribir una sola vez la aplicación y compilarla para las diferentes plataformas móviles objetivo. Sin embargo, estos frameworks están aún en estado muy temprano de desarrollo, por lo que no resuelven toda la problemática ni dan una respuesta completa a los desarrolladores. El objetivo de este Trabajo de Fin de Grado ha sido contribuir a la evolución de estos frameworks mediante la creación de un módulo para Appcelerator Titanium que permita construir de manera ágil aplicaciones multiplataforma que hagan uso de visualizadores de información geográfica. Para ello se propone el desarrollo de un módulo de mapa con soporte para capas WMS, rutas y polígonos en WKT, KML y GeoJSON. Se facilitará además que estas aplicaciones puedan acceder a capacidades del hardware como la brújula y el GPS para realizar un seguimiento de la localización, a la vez que se hace uso de la aceleración por el hardware subyacente para mejorar la velocidad y fluidez de la información visualizada en el mapa. A partir de este módulo se ha creado una aplicación que hace uso de todas sus características y posteriormente se ha migrado a la plataforma Wirecloud4Tablet como componente nativo que puede integrarse con otros componentes web (widgets) mediante técnicas de mashup. Gracias a esto se ha podido fusionar por un lado todas las ventajas que ofrece Wirecloud para el rápido desarrollo de aplicaciones sin necesidad de tener conocimientos de programación, junto con las ventajas que ofrecen las aplicaciones nativas en cuanto a rendimiento y características extras. Usando los resultados de este proyecto, se pueden crear de manera ágil aplicaciones composicionales nativas multiplataforma que hagan uso de visualización de información geográfica; es decir, se pueden crear aplicaciones en pocos minutos y sin conocimientos de programación que pueden ejecutar diferentes componentes (como el mapa) de manera nativa en múltiples plataformas. Se facilita también la integración de componentes nativos (como es el mapa desarrollado) con otros componentes web (widgets) en un mashup que puede visualizarse en dispositivos móviles mediante la plataforma Wirecloud. ---ABSTRACT---In recent years the number of mobile devices and smartphones has increased dramatically as well as the number of applications targeted at them. Developers always have been slowed in the creation of these applications due to the complexity caused by the diversity of operating systems (Android, iOS, Windows Phone, etc), each of them using different programming languages, so that, in order to develop an application that works on these platforms, the developer really has to implement a different application for each platform. To solve this problem frameworks such as Appcelerator Titanium have emerged, allowing developers to write the application once and to compile it for different target mobile platforms. However, these frameworks are still in very early stage of development, so they do not solve all the difficulties nor give a complete solution to the developers. The objective of this final year dissertation is to contribute to the evolution of these frameworks by creating a module for Appcelerator Titanium that permits to nimbly build multi-platform applications that make use of geographical information visualization. To this end, the development of a map module with support for WMS layers, paths, and polygons in WKT, KML, and GeoJSON is proposed. This module will also facilitate these applications to access hardware capabilities such as GPS and compass to track the location, while it makes use of the underlying hardware acceleration to improve the speed and fluidity of the information displayed on the map. Based on this module, it has been created an application that makes use of all its features and subsequently it has been migrated to the platform Wirecloud4Tablet as a native component that can be integrated with other web components (widgets) using mashup techniques. As a result, it has been fused on one side all the advantages Wirecloud provides for fast application development without the need of programming skills, along with the advantages of native apps, such as performance and extra features. Using the results of this project, compositional platform native applications that make use of geographical information visualization can be created in an agile way; ie, in a few minutes and without having programming skills, a developer could create applications that can run different components (like the map) natively on multiple platforms. It also facilitates the integration of native components (like the map) with other web components (widgets) in a mashup that can be displayed on mobile devices through the Wirecloud platform.

Aerial Coverage Path Planning applied to Mapping

In the last decade we have seen how small and light weight aerial platforms - aka, Mini Unmanned Aerial Vehicles (MUAV) - shipped with heterogeneous sensors have become a 'most wanted' Remote Sensing (RS) tool. Most of the off-the-shelf aerial systems found in the market provide way-point navigation. However, they do not rely on a tool that compute the aerial trajectories considering all the aspects that allow optimizing the aerial missions. One of the most demanded RS applications of MUAV is image surveying. The images acquired are typically used to build a high-resolution image, i.e., a mosaic of the workspace surface. Although, it may be applied to any other application where a sensor-based map must be computed. This thesis provides a study of this application and a set of solutions and methods to address this kind of aerial mission by using a fleet of MUAVs. In particular, a set of algorithms are proposed for map-based sampling, and aerial coverage path planning (ACPP). Regarding to map-based sampling, the approaches proposed consider workspaces with different shapes and surface characteristics. The workspace is sampled considering the sensor characteristics and a set of mission requirements. The algorithm applies different computational geometry approaches, providing a unique way to deal with workspaces with different shape and surface characteristics in order to be surveyed by one or more MUAVs. This feature introduces a previous optimization step before path planning. After that, the ACPP problem is theorized and a set of ACPP algorithms to compute the MUAVs trajectories are proposed. The problem addressed herein is the problem to coverage a wide area by using MUAVs with limited autonomy. Therefore, the mission must be accomplished in the shortest amount of time. The aerial survey is usually subject to a set of workspace restrictions, such as the take-off and landing positions as well as a safety distance between elements of the fleet. Moreover, it has to avoid forbidden zones to y. Three different algorithms have been studied to address this problem. The approaches studied are based on graph searching, heuristic and meta-heuristic approaches, e.g., mimic, evolutionary. Finally, an extended survey of field experiments applying the previous methods, as well as the materials and methods adopted in outdoor missions is presented. The reported outcomes demonstrate that the findings attained from this thesis improve ACPP mission for mapping purpose in an efficient and safe manner.

Aerial Coverage Path Planning applied to Mapping

In the last decade we have seen how small and light weight aerial platforms - aka, Mini Unmanned Aerial Vehicles (MUAV) - shipped with heterogeneous sensors have become a 'most wanted' Remote Sensing (RS) tool. Most of the off-the-shelf aerial systems found in the market provide way-point navigation. However, they do not rely on a tool that compute the aerial trajectories considering all the aspects that allow optimizing the aerial missions. One of the most demanded RS applications of MUAV is image surveying. The images acquired are typically used to build a high-resolution image, i.e., a mosaic of the workspace surface. Although, it may be applied to any other application where a sensor-based map must be computed. This thesis provides a study of this application and a set of solutions and methods to address this kind of aerial mission by using a fleet of MUAVs. In particular, a set of algorithms are proposed for map-based sampling, and aerial coverage path planning (ACPP). Regarding to map-based sampling, the approaches proposed consider workspaces with different shapes and surface characteristics. The workspace is sampled considering the sensor characteristics and a set of mission requirements. The algorithm applies different computational geometry approaches, providing a unique way to deal with workspaces with different shape and surface characteristics in order to be surveyed by one or more MUAVs. This feature introduces a previous optimization step before path planning. After that, the ACPP problem is theorized and a set of ACPP algorithms to compute the MUAVs trajectories are proposed. The problem addressed herein is the problem to coverage a wide area by using MUAVs with limited autonomy. Therefore, the mission must be accomplished in the shortest amount of time. The aerial survey is usually subject to a set of workspace restrictions, such as the take-off and landing positions as well as a safety distance between elements of the fleet. Moreover, it has to avoid forbidden zones to y. Three different algorithms have been studied to address this problem. The approaches studied are based on graph searching, heuristic and meta-heuristic approaches, e.g., mimic, evolutionary. Finally, an extended survey of field experiments applying the previous methods, as well as the materials and methods adopted in outdoor missions is presented. The reported outcomes demonstrate that the findings attained from this thesis improve ACPP mission for mapping purpose in an efficient and safe manner.

Auscultación de presas de hormigón con láser escáner terrestre y modelización de las deformaciones del paramento

Se está produciendo en la geodesia un cambio de paradigma en la concepción de los modelos digitales del terreno, pasando de diseñar el modelo con el menor número de puntos posibles a hacerlo con cientos de miles o millones de puntos. Este cambio ha sido consecuencia de la introducción de nuevas tecnologías como el escáner láser, la interferometría radar y el tratamiento de imágenes. La rápida aceptación de estas nuevas tecnologías se debe principalmente a la gran velocidad en la toma de datos, a la accesibilidad por no precisar de prisma y al alto grado de detalle de los modelos. Los métodos topográficos clásicos se basan en medidas discretas de puntos que considerados en su conjunto forman un modelo; su precisión se deriva de la precisión en la toma singular de estos puntos. La tecnología láser escáner terrestre (TLS) supone una aproximación diferente para la generación del modelo del objeto observado. Las nubes de puntos, producto del escaneo con TLS, pasan a ser tratadas en su conjunto mediante análisis de áreas, de forma que ahora el modelo final no es el resultado de una agregación de puntos sino la de la mejor superficie que se adapta a las nubes de puntos. Al comparar precisiones en la captura de puntos singulares realizados con métodos taquimétricos y equipos TLS la inferioridad de estos últimos es clara; sin embargo es en el tratamiento de las nubes de puntos, con los métodos de análisis basados en áreas, se han obtenido precisiones aceptables y se ha podido considerar plenamente la incorporación de esta tecnología en estudios de deformaciones y movimientos de estructuras. Entre las aplicaciones del TLS destacan las de registro del patrimonio, registro de las fases en la construcción de plantas industriales y estructuras, atestados de accidentes y monitorización de movimientos del terreno y deformaciones de estructuras. En la auscultación de presas, comparado con la monitorización de puntos concretos dentro, en coronación o en el paramento de la presa, disponer de un modelo continuo del paramento aguas abajo de la presa abre la posibilidad de introducir los métodos de análisis de deformaciones de superficies y la creación de modelos de comportamiento que mejoren la comprensión y previsión de sus movimientos. No obstante, la aplicación de la tecnología TLS en la auscultación de presas debe considerarse como un método complementario a los existentes. Mientras que los péndulos y la reciente técnica basada en el sistema de posicionamiento global diferencial (DGPS) dan una información continua de los movimientos de determinados puntos de la presa, el TLS permite ver la evolución estacional y detectar posibles zonas problemáticas en todo el paramento. En este trabajo se analizan las características de la tecnología TLS y los parámetros que intervienen en la precisión final de los escaneos. Se constata la necesidad de utilizar equipos basados en la medida directa del tiempo de vuelo, también llamados pulsados, para distancias entre 100 m y 300 m Se estudia la aplicación del TLS a la modelización de estructuras y paramentos verticales. Se analizan los factores que influyen en la precisión final, como el registro de nubes, tipo de dianas y el efecto conjunto del ángulo y la distancia de escaneo. Finalmente, se hace una comparación de los movimientos dados por los péndulos directos de una presa con los obtenidos del análisis de las nubes de puntos correspondientes a varias campañas de escaneos de la misma presa. Se propone y valida el empleo de gráficos patrón para relacionar las variables precisión o exactitud con los factores distancia y ángulo de escaneo en el diseño de trabajos de campo. Se expone su aplicación en la preparación del trabajo de campo para la realización de una campaña de escaneos dirigida al control de movimientos de una presa y se realizan recomendaciones para la aplicación de la técnica TLS a grandes estructuras. Se ha elaborado el gráfico patrón de un equipo TLS concreto de alcance medio. Para ello se hicieron dos ensayos de campo en condiciones reales de trabajo, realizando escaneos en todo el rango de distancias y ángulos de escaneo del equipo. Se analizan dos métodos para obtener la precisión en la modelización de paramentos y la detección de movimientos de estos: el método del “plano de mejor ajuste” y el método de la “deformación simulada”. Por último, se presentan los resultados de la comparación de los movimientos estacionales de una presa arco-gravedad entre los registrados con los péndulos directos y los obtenidos a partir de los escaneos realizados con un TLS. Los resultados muestran diferencias de milímetros, siendo el mejor de ellos del orden de un milímetro. Se explica la metodología utilizada y se hacen consideraciones respecto a la densidad de puntos de las nubes y al tamaño de las mallas de triángulos. A shift of paradigm in the conception of the survey digital models is taking place in geodesy, moving from designing a model with the fewer possible number of points to models of hundreds of thousand or million points. This change has happened because of the introduction of new technologies like the laser scanner, the interferometry radar and the processing of images. The fast acceptance of these new technologies has been due mainly to the great speed getting the data, to the accessibility as reflectorless technique, and to the high degree of detail of the models. Classic survey methods are based on discreet measures of points that, considered them as a whole, form a model; the precision of the model is then derived from the precision measuring the single points. The terrestrial laser scanner (TLS) technology supposes a different approach to the model generation of the observed object. Point cloud, the result of a TLS scan, must be treated as a whole, by means of area-based analysis; so, the final model is not an aggregation of points but the one resulting from the best surface that fits with the point cloud. Comparing precisions between the one resulting from the capture of singular points made with tachometric measurement methods and with TLS equipment, the inferiority of this last one is clear; but it is in the treatment of the point clouds, using area-based analysis methods, when acceptable precisions have been obtained and it has been possible to consider the incorporation of this technology for monitoring structures deformations. Among TLS applications it have to be emphasized those of registry of the cultural heritage, stages registry during construction of industrial plants and structures, police statement of accidents and monitorization of land movements and structures deformations. Compared with the classical dam monitoring, approach based on the registry of a set of points, the fact having a continuous model of the downstream face allows the possibility of introducing deformation analysis methods and behavior models that would improve the understanding and forecast of dam movements. However, the application of TLS technology for dam monitoring must be considered like a complementary method with the existing ones. Pendulums and recently the differential global positioning system (DGPS) give a continuous information of the movements of certain points of the dam, whereas TLS allows following its seasonal evolution and to detect damaged zones of the dam. A review of the TLS technology characteristics and the factors affecting the final precision of the scanning data is done. It is stated the need of selecting TLS based on the direct time of flight method, also called pulsed, for scanning distances between 100m and 300m. Modelling of structures and vertical walls is studied. Factors that influence in the final precision, like the registry of point clouds, target types, and the combined effect of scanning distance and angle of incidence are analyzed. Finally, a comparison among the movements given by the direct pendulums of a dam and the ones obtained from the analysis of point clouds is done. A new approach to obtain a complete map-type plot of the precisions of TLS equipment based on the direct measurement of time of flight method at midrange distances is presented. Test were developed in field-like conditions, similar to dam monitoring and other civil engineering works. Taking advantage of graphic semiological techniques, a “distance - angle of incidence” map based was designed and evaluated for field-like conditions. A map-type plot was designed combining isolines with sized and grey scale points, proportional to the precision values they represent. Precisions under different field conditions were compared with specifications. For this purpose, point clouds were evaluated under two approaches: the standar "plane-of-best-fit" and the proposed "simulated deformation”, that showed improved performance. These results lead to a discussion and recommendations about optimal TLS operation in civil engineering works. Finally, results of the comparison of seasonal movements of an arc-gravity dam between the registered by the direct pendulums ant the obtained from the TLS scans, are shown. The results show differences of millimeters, being the best around one millimeter. The used methodology is explained and considerations with respect to the point cloud density and to the size of triangular meshes are done.

Aplicación de herramientas gis para la cartografía y correlación de datos de ensayos no destructivos en el diagnóstico de edificios históricos

La presente tesis propone un nuevo método de cartografía de ensayos no destructivos en edificios históricos mediante el uso de técnicas basadas en SIG. Primeramente, se define el método por el cual es posible elaborar y convertir una cartografía 3D basada en nubes de puntos de un elemento arquitectónico obtenida mediante fotogrametría, en cartografía raster y vectorial, legible por los sistemas SIG mediante un sistema de coordenadas particular que referencian cada punto de la nube obtenida por fotogrametría. A esta cartografía inicial la denominaremos cartografía base. Después, se define el método por el cual los puntos donde se realiza un ensayo NDT se referencian al sistema de coordenadas del plano base, lo que permite la generación de cartografías de los ensayos referenciadas y la posibilidad de obtener sobre un mismo plano base diferentes datos de múltiples ensayos. Estas nuevas cartografías las denominaremos cartografías de datos, y se demostrará la utilidad de las mismas en el estudio del deterioro y la humedad. Se incluirá el factor tiempo en las cartografías, y se mostrará cómo este nuevo hecho posibilita el trabajo interdisciplinar en la elaboración del diagnóstico. Finalmente, se generarán nuevas cartografías inéditas hasta entonces consistentes en la combinación de diferentes cartografías de datos con la misma planimetría base. Estas nuevas cartografías, darán pie a la obtención de lo que se ha definido como mapas de isograma de humedad, mapa de isograma de salinidad, factor de humedad, factor de evaporación, factor de salinidad y factor de degradación del material. Mediante este sistema se facilitará una mejor visión del conjunto de los datos obtenidos en el estudio del edificio histórico, lo que favorecerá la correcta y rigurosa interpretación de los datos para su posterior restauración. ABSTRACT This research work proposes a new mapping method of non-destructive testing in historical buildings, by using techniques based on GIS. First of all, the method that makes it possible to produce and convert a 3D map based on cloud points from an architectural element obtained by photogrammetry, are defined, as raster and vector, legible by GIS mapping systems using a particular coordinate system that will refer each cloud point obtained by photogrammetry. This initial mapping will be named base planimetry. Afterwards, the method by which the points where the NDT test is performed are referenced to the coordinate system of the base plane , which allows the generation of maps of the referenced tests and the possibility of obtaining different data from multiple tests on the same base plane. These new maps will be named mapping data and their usefulness will be demonstrated in the deterioration and moisture study. The time factor in maps will be included, and how this new fact will enable the interdisciplinary work in the elaboration of the diagnosis will be proved. Finally, new maps (unpublished until now) will be generated by combining different mapping from the same planimetry data base. These new maps will enable us to obtain what have been called isograma moisture maps, isograma salinity- maps, humidity factor, evaporation factor, salinity factor and the material degradation factor. This system will provide a better vision of all data obtained in the study of historical buildings , and will ease the proper and rigorous data interpretation for its subsequent restoration.

Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis

Higher plant reproduction is unique because two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, a tissue that supports embryo development. To understand mechanisms that initiate reproduction, we isolated a mutation in Arabidopsis, f644, that allows for replication of the central cell and subsequent endosperm development without fertilization. When mutant f644 egg and central cells are fertilized by wild-type sperm, embryo development is inhibited, and endosperm is overproduced. By using a map-based strategy, we cloned and sequenced the F644 gene and showed that it encodes a SET-domain polycomb protein. Subsequently, we found that F644 is identical to MEDEA (MEA), a gene whose maternal-derived allele is required for embryogenesis [Grossniklaus, U., Vielle-Calzada, J.-P., Hoeppner, M. A. & Gagliano, W. B. (1998) Science 280, 446–450]. Together, these results reveal functions for plant polycomb proteins in the suppression of central cell proliferation and endosperm development. We discuss models to explain how polycomb proteins function to suppress endosperm and promote embryo development.

Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-SceI

We have investigated physical distances and directions of transposition of the maize transposable element Ac in Arabidopsis thaliana. We prepared a transferred DNA (T-DNA) construct that carried a non-autonomous derivative of Ac with a site for cleavage by endonuclease I-SceI (designated dAc-I-RS element). Another cleavage site was also introduced into the T-DNA region outside dAc-I-RS. Three transgenic Arabidopsis plants were generated, each of which had a single copy of the T-DNA at a different chromosomal location. These transgenic plants were crossed with the Arabidopsis that carried the gene for Ac transposase and progeny in which dAc-I-RS had been transposed were isolated. After digestion of the genomic DNA of these progeny with endonuclease I-SceI, sizes of segment of DNA were determined by pulse-field gel electrophoresis. We also performed linkage analysis for the transposed elements and sites of mutations near the elements. Our results showed that 50% of all transposition events had occurred within 1,700 kb on the same chromosome, with 35% within 200 kb, and that the elements transposed in both directions on the chromosome with roughly equal probability. The data thus indicate that the Ac–Ds system is most useful for tagging of genes that are present within 200 kb of the chromosomal site of Ac in Arabidopsis. In addition, determination of the precise localization of the transposed dAc-I-RS element should definitely assist in map-based cloning of genes around insertion sites.

PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis

The life cycle of angiosperms is punctuated by a dormant phase that separates embryonic and postembryonic development of the sporophyte. In the pickle (pkl) mutant of Arabidopsis, embryonic traits are expressed after germination. The penetrance of the pkl phenotype is strongly enhanced by inhibitors of gibberellin biosynthesis. Map-based cloning of the PKL locus revealed that it encodes a CHD3 protein. CHD3 proteins have been implicated as chromatin-remodeling factors involved in repression of transcription. PKL is necessary for repression of LEC1, a gene implicated as a critical activator of embryo development. We propose that PKL is a component of a gibberellin-modulated developmental switch that functions during germination to prevent reexpression of the embryonic developmental state.

High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: A major fruit weight quantitative trait locus in tomato

A high-resolution physical and genetic map of a major fruit weight quantitative trait locus (QTL), fw2.2, has been constructed for a region of tomato chromosome 2. Using an F2 nearly isogenic line mapping population (3472 individuals) derived from Lycopersicon esculentum (domesticated tomato) × Lycopersicon pennellii (wild tomato), fw2.2 has been placed near TG91 and TG167, which have an interval distance of 0.13 ± 0.03 centimorgan. The physical distance between TG91 and TG167 was estimated to be ≤ 150 kb by pulsed-field gel electrophoresis of tomato DNA. A physical contig composed of six yeast artificial chromosomes (YACs) and encompassing fw2.2 was isolated. No rearrangements or chimerisms were detected within the YAC contig based on restriction fragment length polymorphism analysis using YAC-end sequences and anchored molecular markers from the high-resolution map. Based on genetic recombination events, fw2.2 could be narrowed down to a region less than 150 kb between molecular markers TG91 and HSF24 and included within two YACs: YAC264 (210 kb) and YAC355 (300 kb). This marks the first time, to our knowledge, that a QTL has been mapped with such precision and delimited to a segment of cloned DNA. The fact that the phenotypic effect of the fw2.2 QTL can be mapped to a small interval suggests that the action of this QTL is likely due to a single gene. The development of the high-resolution genetic map, in combination with the physical YAC contig, suggests that the gene responsible for this QTL and other QTLs in plants can be isolated using a positional cloning strategy. The cloning of fw2.2 will likely lead to a better understanding of the molecular biology of fruit development and to the genetic engineering of fruit size characteristics.

Cloning of the Arabidopsis RTM1 gene, which controls restriction of long-distance movement of tobacco etch virus

The locus RTM1 is necessary for restriction of long-distance movement of tobacco etch virus in Arabidopsis thaliana without causing a hypersensitive response or inducing systemic acquired resistance. The RTM1 gene was isolated by map-based cloning. The deduced gene product is similar to the α-chain of the Artocarpus integrifolia lectin, jacalin, and to several proteins that contain multiple repeats of a jacalin-like sequence. These proteins comprise a family with members containing modular organizations of one or more jacalin repeat units and are implicated in defense against viruses, fungi, and insects.

Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.)

For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum, the genome is hexaploid, has a size of 1.6 × 1010 bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed chromosome walking and positional cloning. Here, we demonstrate that chromosome walking using bacterial artificial chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (Am genome). BAC end sequences were mostly repetitive and could not be used for the first walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two walking steps resulted in a physical contig of 450 kb on chromosome 1AmS. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome chromosome walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.

TOM1, an Arabidopsis gene required for efficient multiplication of a tobamovirus, encodes a putative transmembrane protein

Host-encoded factors play an important role in virus multiplication, acting in concert with virus-encoded factors. However, information regarding the host factors involved in this process is limited. Here we report the map-based cloning of an Arabidopsis thaliana gene, TOM1, which is necessary for the efficient multiplication of tobamoviruses, positive-strand RNA viruses infecting a wide variety of plants. The TOM1 mRNA is suggested to encode a 291-aa polypeptide that is predicted to be a multipass transmembrane protein. The Sos recruitment assay supported the hypothesis that TOM1 is associated with membranes, and in addition, that TOM1 interacts with the helicase domain of tobamovirus-encoded replication proteins. Taken into account that the tobamovirus replication complex is associated with membranes, we propose that TOM1 participates in the in vivo formation of the replication complex by serving as a membrane anchor.

Ancient origin of pathogen recognition specificity conferred by the tomato disease resistance gene Pto

We have investigated the origin of the Pto disease resistance (R) gene that was previously identified in the wild tomato species Lycopersicon pimpinellifolium and isolated by map-based cloning. Pto encodes a serine-threonine protein kinase that specifically recognizes strains of Pseudomonas syringae pv. tomato (Pst) that express the avirulence gene avrPto. We examined an accession of the distantly related wild species Lycopersicon hirsutum var. glabratum that exhibits avrPto-specific resistance to Pst. The Pst resistance of L. hirsutum was introgressed into a susceptible Lycopersicon esculentum background to create the near-isogenic line 96T133-3. Resistance to Pst(avrPto) in 96T133-3 was inherited as a single dominant locus and cosegregated with a restriction fragment length polymorphism detected by the Pto gene. This observation suggested that a member of the Pto gene family confers Pst(avrPto) resistance in this L. hirsutum line. Here we report the cloning and characterization of four members of the Pto family from 96T133-3. One gene (LhirPto) is 97% identical to Pto and encodes a catalytically active protein kinase that elicits a hypersensitive response when coexpressed with avrPto in leaves of Nicotiana benthamiana. In common with the Pto kinase, the LhirPto protein physically interacts with AvrPto and downstream members of the Pto signaling pathway. Our studies indicate that R genes of the protein kinase class may not evolve rapidly in response to pathogen pressure and rather that their ability to recognize specific Avr proteins can be highly conserved.