Discrete Multi-Criteria Methods for lands use and conservation planning on La Colacha in Arroyos Menores (Río Cuarto, Province of Córdoba, Argentina)

The study area is La Colacha sub-basins from Arroyos Menores basins, natural areas at West and South of Río Cuarto in Province of Córdoba of Argentina, fertile with loess soils and monsoon temperate climate, but with soil erosions including regressive gullies that degrade them progressively. Cultivated gently since some hundred sixty years, coordinated action planning became necessary to conserve lands while keeping good agro-production. The authors had improved data on soils and on hydrology for the study area, evaluated systems of soil uses and actions to be recommended and applied Decision Support Systems (DSS) tools for that, and were conducted to use discrete multi-criteria models (MCDM) for the more global views about soil conservation and hydraulic management actions and about main types of use of soils. For that they used weighted PROMETHEE, ELECTRE, and AHP methods with a system of criteria grouped as environmental, economic and social, and criteria from their data on effects of criteria. The alternatives resulting offer indication for planning depending somehow on sub basins and on selections of weights, but actions for conservation of soils and water management measures are recommended to conserve the basins conditions, actually sensibly degrading, mainly keeping actual uses of the lands.

Transit Use by Young People in Times of Financial Austerity: A Cause of Equity Concern?

This study investigates the effect of price and travel time fairness and spatial equity in transit provision on the perceived transit service quality, willingness to pay, and habitual frequency of use. Based on the theory of planned behavior, we developed a web-based questionnaire for revealed preferences data collection. The survey was administered among young people in Copenhagen and Lisbon to explore the transit perceptions and use under different economic and transit provision conditions. The survey yielded 499 questionnaires, analyzed by means of structural equation models. Results show that higher perceived fairness relates positively to higher perceived quality of transit service and higher perceived ease of paying for transit use. Higher perceived spatial equity in service provision is associated with higher perceived service quality. Higher perceived service quality relates to higher perceived ease of payment, which links to higher frequency of transit use.

Vector Boolean Functions: Applications in Symmetric Cryptography

Esta tesis establece los fundamentos teóricos y diseña una colección abierta de clases C++ denominada VBF (Vector Boolean Functions) para analizar funciones booleanas vectoriales (funciones que asocian un vector booleano a otro vector booleano) desde una perspectiva criptográfica. Esta nueva implementación emplea la librería NTL de Victor Shoup, incorporando nuevos módulos que complementan a las funciones de NTL, adecuándolas para el análisis criptográfico. La clase fundamental que representa una función booleana vectorial se puede inicializar de manera muy flexible mediante diferentes estructuras de datas tales como la Tabla de verdad, la Representación de traza y la Forma algebraica normal entre otras. De esta manera VBF permite evaluar los criterios criptográficos más relevantes de los algoritmos de cifra en bloque y de stream, así como funciones hash: por ejemplo, proporciona la no-linealidad, la distancia lineal, el grado algebraico, las estructuras lineales, la distribución de frecuencias de los valores absolutos del espectro Walsh o del espectro de autocorrelación, entre otros criterios. Adicionalmente, VBF puede llevar a cabo operaciones entre funciones booleanas vectoriales tales como la comprobación de igualdad, la composición, la inversión, la suma, la suma directa, el bricklayering (aplicación paralela de funciones booleanas vectoriales como la empleada en el algoritmo de cifra Rijndael), y la adición de funciones coordenada. La tesis también muestra el empleo de la librería VBF en dos aplicaciones prácticas. Por un lado, se han analizado las características más relevantes de los sistemas de cifra en bloque. Por otro lado, combinando VBF con algoritmos de optimización, se han diseñado funciones booleanas cuyas propiedades criptográficas son las mejores conocidas hasta la fecha. ABSTRACT This thesis develops the theoretical foundations and designs an open collection of C++ classes, called VBF, designed for analyzing vector Boolean functions (functions that map a Boolean vector to another Boolean vector) from a cryptographic perspective. This new implementation uses the NTL library from Victor Shoup, adding new modules which complement the existing ones making VBF better suited for cryptography. The fundamental class representing a vector Boolean function can be initialized in a flexible way via several alternative types of data structures such as Truth Table, Trace Representation, Algebraic Normal Form (ANF) among others. This way, VBF allows the evaluation of the most relevant cryptographic criteria for block and stream ciphers as well as for hash functions: for instance, it provides the nonlinearity, the linearity distance, the algebraic degree, the linear structures, the frequency distribution of the absolute values of the Walsh Spectrum or the Autocorrelation Spectrum, among others. In addition, VBF can perform operations such as equality testing, composition, inversion, sum, direct sum, bricklayering (parallel application of vector Boolean functions as employed in Rijndael cipher), and adding coordinate functions of two vector Boolean functions. This thesis also illustrates the use of VBF in two practical applications. On the one hand, the most relevant properties of the existing block ciphers have been analysed. On the other hand, by combining VBF with optimization algorithms, new Boolean functions have been designed which have the best known cryptographic properties up-to-date.

Simulation of thermal performance of glazing in architecture using scale models = Simulación del comportamiento térmico de los acristalamientos en la arquitectura mediante modelos a escala

El propósito de esta tesis es estudiar la aproximación a los fenómenos de transporte térmico en edificación acristalada a través de sus réplicas a escala. La tarea central de esta tesis es, por lo tanto, la comparación del comportamiento térmico de modelos a escala con el correspondiente comportamiento térmico del prototipo a escala real. Los datos principales de comparación entre modelo y prototipo serán las temperaturas. En el primer capítulo del Estado del Arte de esta tesis se hará un recorrido histórico por los usos de los modelos a escala desde la antigüedad hasta nuestro días. Dentro de éste, en el Estado de la Técnica, se expondrán los beneficios que tiene su empleo y las dificultades que conllevan. A continuación, en el Estado de la Investigación de los modelos a escala, se analizarán artículos científicos y tesis. Precisamente, nos centraremos en aquellos modelos a escala que son funcionales. Los modelos a escala funcionales son modelos a escala que replican, además, una o algunas de las funciones de sus prototipos. Los modelos a escala pueden estar distorsionados o no. Los modelos a escala distorsionados son aquellos con cambios intencionados en las dimensiones o en las características constructivas para la obtención de una respuesta específica por ejemplo, replicar el comportamiento térmico. Los modelos a escala sin distorsión, o no distorsionados, son aquellos que mantienen, en la medida de lo posible, las proporciones dimensionales y características constructivas de sus prototipos de referencia. Estos modelos a escala funcionales y no distorsionados son especialmente útiles para los arquitectos ya que permiten a la vez ser empleados como elementos funcionales de análisis y como elementos de toma de decisiones en el diseño constructivo. A pesar de su versatilidad, en general, se observará que se han utilizado muy poco estos modelos a escala funcionales sin distorsión para el estudio del comportamiento térmico de la edificación. Posteriormente, se expondrán las teorías para el análisis de los datos térmicos recogidos de los modelos a escala y su aplicabilidad a los correspondientes prototipos a escala real. Se explicarán los experimentos llevados a cabo, tanto en laboratorio como a intemperie. Se han realizado experimentos con modelos sencillos cúbicos a diferentes escalas y sometidos a las mismas condiciones ambientales. De estos modelos sencillos hemos dado el salto a un modelo reducido de una edificación acristalada relativamente sencilla. Los experimentos consisten en ensayos simultáneos a intemperie del prototipo a escala real y su modelo reducido del Taller de Prototipos de la Escuela Técnica Superior de Arquitectura de Madrid (ETSAM). Para el análisis de los datos experimentales hemos aplicado las teorías conocidas, tanto comparaciones directas como el empleo del análisis dimensional. Finalmente, las simulaciones nos permiten comparaciones flexibles con los datos experimentales, por ese motivo, hemos utilizado tanto programas comerciales como un algoritmo de simulación desarrollado ad hoc para esta investigación. Finalmente, exponemos la discusión y las conclusiones de esta investigación. Abstract The purpose of this thesis is to study the approximation to phenomena of heat transfer in glazed buildings through their scale replicas. The central task of this thesis is, therefore, the comparison of the thermal performance of scale models without distortion with the corresponding thermal performance of their full-scale prototypes. Indoor air temperatures of the scale model and the corresponding prototype are the data to be compared. In the first chapter on the State of the Art, it will be shown a broad vision, consisting of a historic review of uses of scale models, from antiquity to our days. In the section State of the Technique, the benefits and difficulties associated with their implementation are presented. Additionally, in the section State of the Research, current scientific papers and theses on scale models are reviewed. Specifically, we focus on functional scale models. Functional scale models are scale models that replicate, additionally, one or some of the functions of their corresponding prototypes. Scale models can be distorted or not. Scale models with distortion are considered scale models with intentional changes, on one hand, in dimensions scaled unevenly and, on the other hand, in constructive characteristics or materials, in order to get a specific performance for instance, a specific thermal performance. Consequently, scale models without distortion, or undistorted scale models scaled evenly, are those replicating, to the extent possible, without distortion, the dimensional proportions and constructive configurations of their prototypes of reference. These undistorted and functional scale models are especially useful for architects because they can be used, simultaneously, as functional elements of analysis and as decision-making elements during the design. Although they are versatile, in general, it is remarkable that these types of models are used very little for the study of the thermal performance of buildings. Subsequently, the theories related to the analysis of the experimental thermal data collected from the scale models and their applicability to the corresponding full-scale prototypes, will be explained. Thereafter, the experiments in laboratory and at outdoor conditions are detailed. Firstly, experiments carried out with simple cube models at different scales are explained. The prototype larger in size and the corresponding undistorted scale model have been subjected to same environmental conditions in every experimental test. Secondly, a step forward is taken carrying out some simultaneous experimental tests of an undistorted scale model, replica of a relatively simple lightweight and glazed building construction. This experiment consists of monitoring the undistorted scale model of the prototype workshop located in the School of Architecture (ETSAM) of the Technical University of Madrid (UPM). For the analysis of experimental data, known related theories and resources are applied, such as, direct comparisons, statistical analyses, Dimensional Analysis and last, but not least important, simulations. Simulations allow us, specifically, flexible comparisons with experimental data. Here, apart the use of the simulation software EnergyPlus, a simulation algorithm is developed ad hoc for this research. Finally, the discussion and conclusions of this research are exposed.

Applications of Formal Languages to Management of Manned and Unmanned Aircraft

En el futuro, la gestión del tráfico aéreo (ATM, del inglés air traffic management) requerirá un cambio de paradigma, de la gestión principalmente táctica de hoy, a las denominadas operaciones basadas en trayectoria. Un incremento en el nivel de automatización liberará al personal de ATM —controladores, tripulación, etc.— de muchas de las tareas que realizan hoy. Las personas seguirán siendo el elemento central en la gestión del tráfico aéreo del futuro, pero lo serán mediante la gestión y toma de decisiones. Se espera que estas dos mejoras traigan un incremento en la eficiencia de la gestión del tráfico aéreo que permita hacer frente al incremento previsto en la demanda de transporte aéreo. Para aplicar el concepto de operaciones basadas en trayectoria, el usuario del espacio aéreo (la aerolínea, piloto, u operador) y el proveedor del servicio de navegación aérea deben negociar las trayectorias mediante un proceso de toma de decisiones colaborativo. En esta negociación, es necesaria una forma adecuada de compartir dichas trayectorias. Compartir la trayectoria completa requeriría un gran ancho de banda, y la trayectoria compartida podría invalidarse si cambiase la predicción meteorológica. En su lugar, podría compartirse una descripción de la trayectoria independiente de las condiciones meteorológicas, de manera que la trayectoria real se pudiese calcular a partir de dicha descripción. Esta descripción de la trayectoria debería ser fácil de procesar usando un programa de ordenador —ya que parte del proceso de toma de decisiones estará automatizado—, pero también fácil de entender para un operador humano —que será el que supervise el proceso y tome las decisiones oportunas—. Esta tesis presenta una serie de lenguajes formales que pueden usarse para este propósito. Estos lenguajes proporcionan los medios para describir trayectorias de aviones durante todas las fases de vuelo, desde la maniobra de push-back (remolcado hasta la calle de rodaje), hasta la llegada a la terminal del aeropuerto de destino. También permiten describir trayectorias tanto de aeronaves tripuladas como no tripuladas, incluyendo aviones de ala fija y cuadricópteros. Algunos de estos lenguajes están estrechamente relacionados entre sí, y organizados en una jerarquía. Uno de los lenguajes fundamentales de esta jerarquía, llamado aircraft intent description language (AIDL), ya había sido desarrollado con anterioridad a esta tesis. Este lenguaje fue derivado de las ecuaciones del movimiento de los aviones de ala fija, y puede utilizarse para describir sin ambigüedad trayectorias de este tipo de aeronaves. Una variante de este lenguaje, denominada quadrotor AIDL (QR-AIDL), ha sido desarrollada en esta tesis para permitir describir trayectorias de cuadricópteros con el mismo nivel de detalle. Seguidamente, otro lenguaje, denominado intent composite description language (ICDL), se apoya en los dos lenguajes anteriores, ofreciendo más flexibilidad para describir algunas partes de la trayectoria y dejar otras sin especificar. El ICDL se usa para proporcionar descripciones genéricas de maniobras comunes, que después se particularizan y combinan para formar descripciones complejas de un vuelo. Otro lenguaje puede construirse a partir del ICDL, denominado flight intent description language (FIDL). El FIDL especifica requisitos de alto nivel sobre las trayectorias —incluyendo restricciones y objetivos—, pero puede utilizar características del ICDL para proporcionar niveles de detalle arbitrarios en las distintas partes de un vuelo. Tanto el ICDL como el FIDL han sido desarrollados en colaboración con Boeing Research & Technology Europe (BR&TE). También se ha desarrollado un lenguaje para definir misiones en las que interactúan varias aeronaves, el mission intent description language (MIDL). Este lenguaje se basa en el FIDL y mantiene todo su poder expresivo, a la vez que proporciona nuevas semánticas para describir tareas, restricciones y objetivos relacionados con la misión. En ATM, los movimientos de un avión en la superficie de aeropuerto también tienen que ser monitorizados y gestionados. Otro lenguaje formal ha sido diseñado con este propósito, llamado surface movement description language (SMDL). Este lenguaje no pertenece a la jerarquía de lenguajes descrita en el párrafo anterior, y se basa en las clearances (autorizaciones del controlador) utilizadas durante las operaciones en superficie de aeropuerto. También proporciona medios para expresar incertidumbre y posibilidad de cambios en las distintas partes de la trayectoria. Finalmente, esta tesis explora las aplicaciones de estos lenguajes a la predicción de trayectorias y a la planificación de misiones. El concepto de trajectory language processing engine (TLPE) se usa en ambas aplicaciones. Un TLPE es una función de ATM cuya principal entrada y salida se expresan en cualquiera de los lenguajes incluidos en la jerarquía descrita en esta tesis. El proceso de predicción de trayectorias puede definirse como una combinación de TLPEs, cada uno de los cuales realiza una pequeña sub-tarea. Se le ha dado especial importancia a uno de estos TLPEs, que se encarga de generar el perfil horizontal, vertical y de configuración de la trayectoria. En particular, esta tesis presenta un método novedoso para la generación del perfil vertical. El proceso de planificar una misión también se puede ver como un TLPE donde la entrada se expresa en MIDL y la salida consiste en cierto número de trayectorias —una por cada aeronave disponible— descritas utilizando FIDL. Se ha formulado este problema utilizando programación entera mixta. Además, dado que encontrar caminos óptimos entre distintos puntos es un problema fundamental en la planificación de misiones, también se propone un algoritmo de búsqueda de caminos. Este algoritmo permite calcular rápidamente caminos cuasi-óptimos que esquivan todos los obstáculos en un entorno urbano. Los diferentes lenguajes formales definidos en esta tesis pueden utilizarse como una especificación estándar para la difusión de información entre distintos actores de la gestión del tráfico aéreo. En conjunto, estos lenguajes permiten describir trayectorias con el nivel de detalle necesario en cada aplicación, y se pueden utilizar para aumentar el nivel de automatización explotando esta información utilizando sistemas de soporte a la toma de decisiones. La aplicación de estos lenguajes a algunas funciones básicas de estos sistemas, como la predicción de trayectorias, han sido analizadas. ABSTRACT Future air traffic management (ATM) will require a paradigm shift from today’s mainly tactical ATM to trajectory-based operations (TBOs). An increase in the level of automation will also relieve humans —air traffic control officers (ATCOs), flight crew, etc.— from many of the tasks they perform today. Humans will still be central in this future ATM, as decision-makers and managers. These two improvements (TBOs and increased automation) are expected to provide the increase in ATM performance that will allow coping with the expected increase in air transport demand. Under TBOs, trajectories are negotiated between the airspace user (an airline, pilot, or operator) and the air navigation service provider (ANSP) using a collaborative decision making (CDM) process. A suitable method for sharing aircraft trajectories is necessary for this negotiation. Sharing a whole trajectory would require a high amount of bandwidth, and the shared trajectory might become invalid if the weather forecast changed. Instead, a description of the trajectory, decoupled from the weather conditions, could be shared, so that the actual trajectory could be computed from this trajectory description. This trajectory description should be easy to process using a computing program —as some of the CDM processes will be automated— but also easy to understand for a human operator —who will be supervising the process and making decisions. This thesis presents a series of formal languages that can be used for this purpose. These languages provide the means to describe aircraft trajectories during all phases of flight, from push back to arrival at the gate. They can also describe trajectories of both manned and unmanned aircraft, including fixedwing and some rotary-wing aircraft (quadrotors). Some of these languages are tightly interrelated and organized in a language hierarchy. One of the key languages in this hierarchy, the aircraft intent description language (AIDL), had already been developed prior to this thesis. This language was derived from the equations of motion of fixed-wing aircraft, and can provide an unambiguous description of fixed-wing aircraft trajectories. A variant of this language, the quadrotor AIDL (QR-AIDL), is developed in this thesis to allow describing a quadrotor aircraft trajectory with the same level of detail. Then, the intent composite description language (ICDL) is built on top of these two languages, providing more flexibility to describe some parts of the trajectory while leaving others unspecified. The ICDL is used to provide generic descriptions of common aircraft manoeuvres, which can be particularized and combined to form complex descriptions of flight. Another language is built on top of the ICDL, the flight intent description language (FIDL). The FIDL specifies high-level requirements on trajectories —including constraints and objectives—, but can use features of the ICDL to provide arbitrary levels of detail in different parts of the flight. The ICDL and FIDL have been developed in collaboration with Boeing Research & Technology Europe (BR&TE). Also, the mission intent description language (MIDL) has been developed to allow describing missions involving multiple aircraft. This language is based on the FIDL and keeps all its expressive power, while it also provides new semantics for describing mission tasks, mission objectives, and constraints involving several aircraft. In ATM, the movement of aircraft while on the airport surface also has to be monitored and managed. Another formal language has been designed for this purpose, denoted surface movement description language (SMDL). This language does not belong to the language hierarchy described above, and it is based on the clearances used in airport surface operations. Means to express uncertainty and mutability of different parts of the trajectory are also provided. Finally, the applications of these languages to trajectory prediction and mission planning are explored in this thesis. The concept of trajectory language processing engine (TLPE) is used in these two applications. A TLPE is an ATM function whose main input and output are expressed in any of the languages in the hierarchy described in this thesis. A modular trajectory predictor is defined as a combination of multiple TLPEs, each of them performing a small subtask. Special attention is given to the TLPE that builds the horizontal, vertical, and configuration profiles of the trajectory. In particular, a novel method for the generation of the vertical profile is presented. The process of planning a mission can also be seen as a TLPE, where the main input is expressed in the MIDL and the output consists of a number of trajectory descriptions —one for each aircraft available in the mission— expressed in the FIDL. A mixed integer linear programming (MILP) formulation for the problem of assigning mission tasks to the available aircraft is provided. In addition, since finding optimal paths between locations is a key problem to mission planning, a novel path finding algorithm is presented. This algorithm can compute near-shortest paths avoiding all obstacles in an urban environment in very short times. The several formal languages described in this thesis can serve as a standard specification to share trajectory information among different actors in ATM. In combination, these languages can describe trajectories with the necessary level of detail for any application, and can be used to increase automation by exploiting this information using decision support tools (DSTs). Their applications to some basic functions of DSTs, such as trajectory prediction, have been analized.

Construction of hybrid proteins that migrate retrogradely and transynaptically into the central nervous system

The nontoxic proteolytic C fragment of tetanus toxin (TTC peptide) has the same ability to bind nerve cells and be retrogradely transported through a synapse as the native toxin. We have investigated its potential use as an in vivo neurotropic carrier. In this work we show that a hybrid protein encoded by the lacZ–TTC gene fusion retains the biological functions of both proteins in vivo—i.e., retrograde transynaptic transport of the TTC fragment and β-galactosidase enzymatic activity. After intramuscular injection, enzymatic activity could be detected in motoneurons and connected neurons of the brainstem areas. This strategy could be used to deliver a biological activity to neurons from the periphery to the central nervous system. Such a hybrid protein could also be used to map synaptic connections between neural cells.

Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags

A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue. To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L. × tremuloides Michx. and Populus trichocarpa ‘Trichobel.’ The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries. Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs showed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

Multiple Functions for Actin during Filamentous Growth of Saccharomyces cerevisiaeV⃞

Saccharomyces cerevisiae is dimorphic and switches from a yeast form to a pseudohyphal (PH) form when starved for nitrogen. PH cells are elongated, bud in a unipolar manner, and invade the agar substrate. We assessed the requirements for actin in mediating the dramatic morphogenetic events that accompany the transition to PH growth. Twelve “alanine scan” alleles of the single yeast actin gene (ACT1) were tested for effects on filamentation, unipolar budding, agar invasion, and cell elongation. Some act1 mutations affect all phenotypes, whereas others affect only one or two aspects of PH growth. Tests of intragenic complementation among specific act1 mutations support the phenotypic evidence for multiple actin functions in filamentous growth. We present evidence that interaction between actin and the actin-binding protein fimbrin is important for PH growth and suggest that association of different actin-binding proteins with actin mediates the multiple functions of actin in filamentous growth. Furthermore, characterization of cytoskeletal structure in wild type and act1/act1 mutants indicates that PH cell morphogenesis requires the maintenance of a highly polarized actin cytoskeleton. Collectively, this work demonstrates that actin plays a central role in fungal dimorphism.

Functional Hierarchy of Simultaneously Expressed Adhesion Receptors: Integrin α2β1 but Not CD44 Mediates MV3 Melanoma Cell Migration and Matrix Reorganization within Three-dimensional Hyaluronan-containing Collagen MatricesV⃞

Haptokinetic cell migration across surfaces is mediated by adhesion receptors including β1 integrins and CD44 providing adhesion to extracellular matrix (ECM) ligands such as collagen and hyaluronan (HA), respectively. Little is known, however, about how such different receptor systems synergize for cell migration through three-dimensionally (3-D) interconnected ECM ligands. In highly motile human MV3 melanoma cells, both β1 integrins and CD44 are abundantly expressed, support migration across collagen and HA, respectively, and are deposited upon migration, whereas only β1 integrins but not CD44 redistribute to focal adhesions. In 3-D collagen lattices in the presence or absence of HA and cross-linking chondroitin sulfate, MV3 cell migration and associated functions such as polarization and matrix reorganization were blocked by anti-β1 and anti-α2 integrin mAbs, whereas mAbs blocking CD44, α3, α5, α6, or αv integrins showed no effect. With use of highly sensitive time-lapse videomicroscopy and computer-assisted cell tracking techniques, promigratory functions of CD44 were excluded. 1) Addition of HA did not increase the migratory cell population or its migration velocity, 2) blocking of the HA-binding Hermes-1 epitope did not affect migration, and 3) impaired migration after blocking or activation of β1 integrins was not restored via CD44. Because α2β1-mediated migration was neither synergized nor replaced by CD44–HA interactions, we conclude that the biophysical properties of 3-D multicomponent ECM impose more restricted molecular functions of adhesion receptors, thereby differing from haptokinetic migration across surfaces.

The Rho-GEF Rom2p Localizes to Sites of Polarized Cell Growth and Participates in Cytoskeletal Functions in Saccharomyces cerevisiae

Rom2p is a GDP/GTP exchange factor for Rho1p and Rho2p GTPases; Rho proteins have been implicated in control of actin cytoskeletal rearrangements. ROM2 and RHO2 were identified in a screen for high-copy number suppressors of cik1Δ, a mutant defective in microtubule-based processes in Saccharomyces cerevisiae. A Rom2p::3XHA fusion protein localizes to sites of polarized cell growth, including incipient bud sites, tips of small buds, and tips of mating projections. Disruption of ROM2 results in temperature-sensitive growth defects at 11°C and 37°C. rom2Δ cells exhibit morphological defects. At permissive temperatures, rom2Δ cells often form elongated buds and fail to form normal mating projections after exposure to pheromone; at the restrictive temperature, small budded cells accumulate. High-copy number plasmids containing either ROM2 or RHO2 suppress the temperature-sensitive growth defects of cik1Δ and kar3Δ strains. KAR3 encodes a kinesin-related protein that interacts with Cik1p. Furthermore, rom2Δ strains exhibit increased sensitivity to the microtubule depolymerizing drug benomyl. These results suggest a role for Rom2p in both polarized morphogenesis and functions of the microtubule cytoskeleton.

Drosophila coracle, a Member of the Protein 4.1 Superfamily, Has Essential Structural Functions in the Septate Junctions and Developmental Functions in Embryonic and Adult Epithelial Cells

Although extensively studied biochemically, members of the Protein 4.1 superfamily have not been as well characterized genetically. Studies of coracle, a Drosophila Protein 4.1 homologue, provide an opportunity to examine the genetic functions of this gene family. coracle was originally identified as a dominant suppressor of EgfrElp, a hypermorphic form of the Drosophila Epidermal growth factor receptor gene. In this article, we present a phenotypic analysis of coracle, one of the first for a member of the Protein 4.1 superfamily. Screens for new coracle alleles confirm the null coracle phenotype of embryonic lethality and failure in dorsal closure, and they identify additional defects in the embryonic epidermis and salivary glands. Hypomorphic coracle alleles reveal functions in many imaginal tissues. Analysis of coracle mutant cells indicates that Coracle is a necessary structural component of the septate junction required for the maintenance of the transepithelial barrier but is not necessary for apical–basal polarity, epithelial integrity, or cytoskeletal integrity. In addition, coracle phenotypes suggest a specific role in cell signaling events. Finally, complementation analysis provides information regarding the functional organization of Coracle and possibly other Protein 4.1 superfamily members. These studies provide insights into a range of in vivo functions for coracle in developing embryos and adults.

The dynamins: Redundant or distinct functions for an expanding family of related GTPases?

In the 7 years since dynamin was first isolated from bovine brain in search of novel microtubule-based motors, our understanding of this enzyme has expanded significantly. We now know that brain dynamin belongs to a family of large GTPases, which mediate vesicle trafficking. Furthermore, this enzymatic activity is markedly increased through association with microtubules, acidic phospholipids, and certain regulatory proteins that contain Src homology 3 (SH3) domains. From functional, genetic, and cellular manipulations, it is now generally accepted that dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event. These observations have confirmed at least one function of dynamin that was predicted from seminal studies on a pleiotropic mutant, shibirets (shits) in Drosophila melanogaster. Of equal interest is the finding that there are multiple dynamin gene products, including two that are expressed in a tissue-specific manner, and they share marked homology with a larger family of distinct but related proteins. Therefore, it is attractive to speculate that the different dynamins may participate in related cellular functions, such as distinct endocytic processes and even secretion. In turn, dynamin could play an important role in cell growth, cell spreading, and neurite outgrowth. The purpose of this review is to enumerate on the expansive dynamin literature and to discuss the nomenclature, expression, and putative functions of this growing and interesting family of proteins.

Synaptic regulation of protein synthesis and the fragile X protein

Protein synthesis occurs in neuronal dendrites, often near synapses. Polyribosomal aggregates often appear in dendritic spines, particularly during development. Polyribosomal aggregates in spines increase during experience-dependent synaptogenesis, e.g., in rats in a complex environment. Some protein synthesis appears to be regulated directly by synaptic activity. We use “synaptoneurosomes,” a preparation highly enriched in pinched-off, resealed presynaptic processes attached to resealed postsynaptic processes that retain normal functions of neurotransmitter release, receptor activation, and various postsynaptic responses including signaling pathways and protein synthesis. We have found that, when synaptoneurosomes are stimulated with glutamate or group I metabotropic glutamate receptor agonists such as dihydroxyphenylglycine, mRNA is rapidly taken up into polyribosomal aggregates, and labeled methionine is incorporated into protein. One of the proteins synthesized is FMRP, the protein that is reduced or absent in fragile X mental retardation syndrome. FMRP has three RNA-binding domains and reportedly binds to a significant number of mRNAs. We have found that dihydroxyphenylglycine-activated protein synthesis in synaptoneurosomes is dramatically reduced in a knockout mouse model of fragile X syndrome, which cannot produce full-length FMRP, suggesting that FMRP is involved in or required for this process. Studies of autopsy samples from patients with fragile X syndrome have indicated that dendritic spines may fail to assume a normal mature size and shape and that there are more spines per unit dendrite length in the patient samples. Similar findings on spine size and shape have come from studies of the knockout mouse. Study of the development of the somatosensory cortical region containing the barrel-like cell arrangements that process whisker information suggests that normal dendritic regression is impaired in the knockout mouse. This finding suggests that FMRP may be required for the normal processes of maturation and elimination to occur in cerebral cortical development.

Dynamic Localization of the Swe1 Regulator Hsl7 During the Saccharomyces cerevisiae Cell Cycle

In Saccharomyces cerevisiae, entry into mitosis requires activation of the cyclin-dependent kinase Cdc28 in its cyclin B (Clb)-associated form. Clb-bound Cdc28 is susceptible to inhibitory tyrosine phosphorylation by Swe1 protein kinase. Swe1 is itself negatively regulated by Hsl1, a Nim1-related protein kinase, and by Hsl7, a presumptive protein-arginine methyltransferase. In vivo all three proteins localize to the bud neck in a septin-dependent manner, consistent with our previous proposal that formation of Hsl1-Hsl7-Swe1 complexes constitutes a checkpoint that monitors septin assembly. We show here that Hsl7 is phosphorylated by Hsl1 in immune-complex kinase assays and can physically associate in vitro with either Hsl1 or Swe1 in the absence of any other yeast proteins. With the use of both the two-hybrid method and in vitro binding assays, we found that Hsl7 contains distinct binding sites for Hsl1 and Swe1. A differential interaction trap approach was used to isolate four single-site substitution mutations in Hsl7, which cluster within a discrete region of its N-terminal domain, that are specifically defective in binding Hsl1. When expressed in hsl7Δ cells, each of these Hsl7 point mutants is unable to localize at the bud neck and cannot mediate down-regulation of Swe1, but retains other functions of Hsl7, including oligomerization and association with Swe1. GFP-fusions of these Hsl1-binding defective Hsl7 proteins localize as a bright perinuclear dot, but never localize to the bud neck; likewise, in hsl1Δ cells, a GFP-fusion to wild-type Hsl7 or native Hsl7 localizes to this dot. Cell synchronization studies showed that, normally, Hsl7 localizes to the dot, but only in cells in the G1 phase of the cell cycle. Immunofluorescence analysis and immunoelectron microscopy established that the dot corresponds to the outer plaque of the spindle pole body (SPB). These data demonstrate that association between Hsl1 and Hsl7 at the bud neck is required to alleviate Swe1-imposed G2-M delay. Hsl7 localization at the SPB during G1 may play some additional role in fine-tuning the coordination between nuclear and cortical events before mitosis.

Interactions of a Rel protein with its inhibitor.

Cactus, a Drosophila homologue of I kappa B, binds to and inhibits Dorsal, a homologue of the p50 and p65 components of NF-kappa B. We describe experiments in yeast with various Dorsal and Cactus derivatives showing that Cactus blocks the DNA binding and nuclear localization functions of Dorsal. In contrast, Dorsal's transcriptional activating region is functional in the Dorsal-Cactus complex. We identify two Dorsal mutants, Dorsal C233R and Dorsal S234P, that escape Cactus inhibition in vivo, and we show that these mutants fail to interact with Cactus in vitro. From this and data of others, we identify the likely surface of Dorsal that binds Cactus. We also describe a modified PCR mutagenesis procedure, easier to use than conventional methods, that produces a library of high complexity.