Regulation of integrin-mediated cellular responses through assembly of a CAS/Crk scaffold

AbstractThe molecular coupling of CAS and Crk in response to integrin activation is an evolutionary conserved signaling module that controls cell proliferation, survival and migration. However, when deregulated, CAS/Crk signaling also contributes to cancer progression and developmental defects in humans. Here we highlight recent advances in our understanding of how CAS/Crk complexes assemble in cells to modulate the actin cytoskeleton, and the molecular mechanisms that regulate this process. We discuss in detail the spatiotemporal dynamics of CAS/Crk assembly and how this scaffold recruits specific effector proteins that couple integrin signaling networks to the migration machinery of cells. We also highlight the importance of CAS/Crk signaling in the dual regulation of cell migration and survival mechanisms that operate in invasive cells during development and pathological conditions associated with cancer metastasis

Heterogeneous verification of model transformations

Esta tesis trata sobre la verificación formal en el contexto de la Ingeniería Dirigida por Modelos (MDE por sus siglas en inglés). El paradigma propone un ciclo de vida de la ingeniería de software basado en una abstracción de su complejidad a través de la definición de modelos y en un proceso de construcción (semi)automático guiado por transformaciones de estos modelos. Nuestro propósito es abordar la verificación de transformaciones de modelos la cual incluye, por extensión, la verificación de sus modelos. Comenzamos analizando la literatura relacionada con la verificación de transformaciones de modelos para concluir que la heterogeneidad de las propiedades que interesa verificar y de los enfoques para hacerlo, sugiere la necesidad de utilizar diversos dominios lógicos, lo cual es la base de nuestra propuesta. En algunos casos puede ser necesario realizar una verificación heterogénea, es decir, utilizar diferentes formalismos para la verificación de cada una de las partes del problema completo. Además, es beneficioso permitir a los expertos formales elegir el dominio en el que se encuentran más capacitados para llevar a cabo una prueba formal. El principal problema reside en que el mantenimiento de múltiples representaciones formales de los elementos de MDE en diferentes dominios lógicos, puede ser costoso si no existe soporte automático o una relación formal clara entre estas representaciones. Motivados por esto, definimos un entorno unificado que permite la verificación formal transformaciones de modelos mediante el uso de métodos de verificación heterogéneos, de forma tal que es posible automatizar la traducción formal de los elementos de MDE entre dominios logicos. Nos basamos formalmente en la Teoría de Instituciones, la cual proporciona una base sólida para la representación de los elementos de MDE (a través de instituciones) sin depender de ningúningún dominio lógico específico. También proporciona una forma de especificar traducciones (a través de comorfismos) que preservan la semántica entre estos elementos y otros dominios lógicos. Nos basamos en estándares para la especificación de los elementos de MDE. De hecho, definimos una institución para la buena formación de los modelos especificada con una versión simplificada del MetaObject Facility y otra institución para transformaciones utilizando Query/View/Transformation Relations. No obstante, la idea puede ser generalizada a otros enfoques de transformación y lenguajes.Por último, demostramos la viabilidad del entorno mediante el desarrollo de un prototipo funcional soportado por el Heterogeneous Tool Set (HETS). HETS permite realizar una especificación heterogénea y provee facilidades para el monitoreo de su corrección global. Los elementos de MDE se conectan con otras lógicas ya soportadas en HETS (por ejemplo: lógica de primer orden, lógica modal, entre otras) a través del Common Algebraic Specification Language (CASL). Esta conexión se expresa teóricamente mediante comorfismos desde las instituciones de MDE a la institución subyacente en CASL. Finalmente, discutimos las principales contribuciones de la tesis. Esto deriva en futuras líneas de investigación que contribuyen a la adopción de métodos formales para la verificación en el contexto de MDE.This thesis is about formal verification in the context of the Model-Driven Engineering (MDE) paradigm. The paradigm proposes a software engineering life-cycle based on an abstraction from its complexity by defining models, and on a (semi)automatic construction process driven by model transformations. Our purpose is to address the verification of model transformations which includes, by extension, the verification of their models. We first review the literature on the verification of model transformations to conclude that the heterogeneity we find in the properties of interest to verify, and in the verification approaches, suggests the need of using different logical domains, which is the base of our proposal. In some cases it can be necessary to perform a heterogeneous verification, i.e. using different formalisms for the verification of each part of the whole problem. Moreover, it is useful to allow formal experts to choose the domain in which they are more skilled to address a formal proof. The main problem is that the maintenance of multiple formal representations of the MDE elements in different logical domains, can be expensive if there is no automated assistance or a clear formal relation between these representations. Motivated by this, we define a unified environment that allows formal verification of model transformations using heterogeneous verification approaches, in such a way that the formal translations of the MDE elements between logical domains can be automated. We formally base the environment on the Theory of Institutions, which provides a sound basis for representing MDE elements (as so called institutions) without depending on any specific logical domain. It also provides a way for specifying semantic-preserving translations (as so called comorphisms) from these elements to other logical domains. We use standards for the specification of the MDE elements. In fact, we define an institution for the well-formedness of models specified with a simplified version of the MetaObject Facility, and another institution for Query/View/Transformation Relations transformations. However, the idea can be generalized to other transformation approaches and languages. Finally, we evidence the feasibility of the environment by the development of a functional prototype supported by the Heterogeneous Tool Set (HETS). HETS supports heterogeneous specifications and provides capabilities for monitoring their overall correctness. The MDE elements are connected to the other logics already supported in HETS (e.g. first-order logic, modal logic, among others) through the Common Algebraic Specification Language (CASL). This connection is defined by means of comorphisms from the MDE institutions to the underlying institution of CASL. We carry out a final discussion of the main contributions of this thesis. This results in future research directions which contribute with the adoption of formal tools for the verification in the context of MDE

Structure-function studies of MICAL, the unusual multidomain flavoenzyme involved in actin cytoskeleton dynamics

MICAL (from the Molecule Interacting with CasL) indicates a family of multidomain proteins conserved from insects to humans, which are increasingly attracting attention for their participation in the control of actin cytoskeleton dynamics, and, therefore, in the several related key processes in health and disease. MICAL is unique among actin binding proteins because it catalyzes a NADPH-dependent F-actin depolymerizing reaction. This unprecedented reaction is associated with its N-terminal FAD-containing domain that is structurally related to p-hydroxybenzoate hydroxylase, the prototype of aromatic monooxygenases, but catalyzes a strong NADPH oxidase activity in the free state. This review will focus on the known structural and functional properties of MICAL forms in order to provide an overview of the arguments supporting the current hypotheses on the possible mechanism of action of MICAL in the free and F-actin bound state, on the modulating effect of the CH, LIM, and C-terminal domains that follow the catalytic flavoprotein domain on the MICAL activities, as well as that of small molecules and proteins interacting with MICAL

Imaging changes in the rodent brain using diffusion weighted multiple boli arterial spin labelling

This thesis combines the quantification of a new arterial spin labelling (ASL) sequence, and the development of a diffusion weighted ASL (DWASL) sequence, to examine blood brain barrier (BBB) impairment. The blood brain barrier maintains the delicate neuroenvironment in the brain by controlling influx and efflux of cells and molecules. Many neurological disorders are effected by an impairment of the BBB. Current magnetic resonance imaging (MRI) methods to image BBB dysfunction involve the use of a contrast agent, which is invasive and not sensitive to subtle changes in BBB permeability. Non-invasive MR methods such as ASL, are able to measure perfusion and produce cerebral blood flow (CBF) maps of the brain. ASL however has an inherently low signal and therefore development of high signal-tonoise ratio (SNR) sequences are needed. Multiple boli ASL (mbASL) is a high SNR sequence that would be suitable for producing CBF maps but lacks quantification. Human African trypanosomiasis (HAT), a parasitic disease native to Africa, results in a progressive diffuse impairment of the BBB throughout the disease course. A murine model of HAT was used to examine water exchange and cerebral blood flow changes with DWASL. Chapter 1 outlines the current literature on the blood brain barrier, HAT and splenomegaly. Chapter 2 introduces the theory of MRI, which is the imaging method used throughout the thesis. Chapter 3 provides a literature review of the ASL sequence and subsequent development of diffusion weighted ASL. The review outlines the main ASL sequences and introduces multiple boli ASL, followed by diffusion weighted ASL. These two sequences are used throughout this thesis. Chapter 4, the first results chapter, experimentally validates the quantification of the mbASL sequence. Chapter 5 outlines the development of diffusion weighted mbASL which could potentially image changes in water exchange across the BBB. Chapter 6 and Chapter 7 use the HAT mouse model first to examine changes in the water exchange in the brain and then to serially image changes in spleen volume