The MIS 5 palaeoenvironmental record in the SE Mediterranean coast of the Iberian Peninsula (Río Antas, Almería, Spain)

Se realiza un estudio detallado del episodio cálido MIS 5 en la zona sureste de la Península Ibérica. Se realiza la reconstrucción paleoambiental a partir del estudio polínico y biomarcadores de un sondeo perforado en la costa de Almería. La cronología se estableció a partir del método de racemizaciónd e aminoácidos.Landwards of a MIS5 bar, a borehole core (SRA) was analyzed to establish the relationship between the lagoonal record and the raised beach deposits in the surroundings of the Antas river mouth and to reconstruct the Pleistocene palaeoenvironmental evolution 5 of the southern Mediterranean coast of the Iberian Peninsula. 63 samples were recovered for amino acid racemization dating, 86 samples for sedimentological and paleontological determination, 37 samples for pollen identification and 54 for biomarker analysis. AAR revealed that the borehole record contains MIS11, MIS6 and MIS5 deposits, the latter extensively represented. During the end of MIS6 and MIS5, a sand 10 barrier developed and created a shallow lagoon with alternating terrestrial inputs this process being common in other Mediterranean realms. Litho- and biofacies allowed the identification of distinct paleoenvironments through time, with the presence of a lagoonal environment alternating with alluvial fan progradation. Biomarkers indicated constant input from terrestrial plants, together with variable development of aquatic 15 macrophytes. The palynological content allowed the reconstruction of the paleoclimatological conditions during MIS6 and 5, with evidence of seven scenarios characterized by alternating arid and relatively humid conditions

Método computacional para la aceleración de análisis paramétricos de modificaciones locales en estructuras complejas sometidas a cargas dinámicas

Dentro del análisis y diseño estructural surgen frecuentemente problemas de ingeniería donde se requiere el análisis dinámico de grandes modelos de elementos finitos que llegan a millones de grados de libertad y emplean volúmenes de datos de gran tamaño. La complejidad y dimensión de los análisis se dispara cuando se requiere realizar análisis paramétricos. Este problema se ha abordado tradicionalmente desde diversas perspectivas: en primer lugar, aumentando la capacidad tanto de cálculo como de memoria de los sistemas informáticos empleados en los análisis. En segundo lugar, se pueden simplificar los análisis paramétricos reduciendo su número o detalle y por último se puede recurrir a métodos complementarios a los elementos .nitos para la reducción de sus variables y la simplificación de su ejecución manteniendo los resultados obtenidos próximos al comportamiento real de la estructura. Se propone el empleo de un método de reducción que encaja en la tercera de las opciones y consiste en un análisis simplificado que proporciona una solución para la respuesta dinámica de una estructura en el subespacio modal complejo empleando un volumen de datos muy reducido. De este modo se pueden realizar análisis paramétricos variando múltiples parámetros, para obtener una solución muy aproximada al objetivo buscado. Se propone no solo la variación de propiedades locales de masa, rigidez y amortiguamiento sino la adición de grados de libertad a la estructura original para el cálculo de la respuesta tanto permanente como transitoria. Adicionalmente, su facilidad de implementación permite un control exhaustivo sobre las variables del problema y la implementación de mejoras como diferentes formas de obtención de los autovalores o la eliminación de las limitaciones de amortiguamiento en la estructura original. El objetivo del método se puede considerar similar a los que se obtienen al aplicar el método de Guyan u otras técnicas de reducción de modelos empleados en dinámica estructural. Sin embargo, aunque el método permite ser empleado en conjunción con otros para obtener las ventajas de ambos, el presente procedimiento no realiza la condensación del sistema de ecuaciones, sino que emplea la información del sistema de ecuaciones completa estudiando tan solo la respuesta en las variables apropiadas de los puntos de interés para el analista. Dicho interés puede surgir de la necesidad de obtener la respuesta de las grandes estructuras en unos puntos determinados o de la necesidad de modificar la estructura en zonas determinadas para cambiar su comportamiento (respuesta en aceleraciones, velocidades o desplazamientos) ante cargas dinámicas. Por lo tanto, el procedimiento está particularmente indicado para la selección del valor óptimo de varios parámetros en grandes estructuras (del orden de cientos de miles de modos) como pueden ser la localización de elementos introducidos, rigideces, masas o valores de amortiguamientos viscosos en estudios previos en los que diversas soluciones son planteadas y optimizadas, y que en el caso de grandes estructuras, pueden conllevar un número de simulaciones extremadamente elevado para alcanzar la solución óptima. Tras plantear las herramientas necesarias y desarrollar el procedimiento, se propone un caso de estudio para su aplicación al modelo de elementos .nitos del UAV MILANO desarrollado por el Instituto Nacional de Técnica Aeroespacial. A dicha estructura se le imponen ciertos requisitos al incorporar un equipo en aceleraciones en punta de ala izquierda y desplazamientos en punta de ala derecha en presencia de la sustentación producida por una ráfaga continua de viento de forma sinusoidal. La modificación propuesta consiste en la adición de un equipo en la punta de ala izquierda, bien mediante un anclaje rígido, bien unido mediante un sistema de reducción de la respuesta dinámica con propiedades de masa, rigidez y amortiguamiento variables. El estudio de los resultados obtenidos permite determinar la optimización de los parámetros del sistema de atenuación por medio de múltiples análisis dinámicos de forma que se cumplan de la mejor forma posible los requisitos impuestos con la modificación. Se comparan los resultados con los obtenidos mediante el uso de un programa comercial de análisis por el método de los elementos .nitos lográndose soluciones muy aproximadas entre el modelo completo y el reducido. La influencia de diversos factores como son el amortiguamiento modal de la estructura original, el número de modos retenidos en la truncatura o la precisión proporcionada por el barrido en frecuencia se analiza en detalle para, por último, señalar la eficiencia en términos de tiempo y volumen de datos de computación que ofrece el método propuesto en comparación con otras aproximaciones. Por lo tanto, puede concluirse que el método propuesto se considera una opción útil y eficiente para el análisis paramétrico de modificaciones locales en grandes estructuras. ABSTRACT When developing structural design and analysis some projects require dynamic analysis of large finite element models with millions of degrees of freedom which use large size data .les. The analysis complexity and size grow if a parametric analysis is required. This problem has been approached traditionally in several ways: one way is increasing the power and the storage capacity of computer systems involved in the analysis. Other obvious way is reducing the total amount of analyses and their details. Finally, complementary methods to finite element analysis can also be employed in order to limit the number of variables and to reduce the execution time keeping the results as close as possible to the actual behaviour of the structure. Following this third option, we propose a model reduction method that is based in a simplified analysis that supplies a solution for the dynamic response of the structure in the complex modal space using few data. Thereby, parametric analysis can be done varying multiple parameters so as to obtain a solution which complies with the desired objetive. We propose not only mass, stiffness and damping variations, but also addition of degrees of freedom to the original structure in order to calculate the transient and steady-state response. Additionally, the simple implementation of the procedure allows an in-depth control of the problem variables. Furthermore, improvements such as different ways to obtain eigenvectors or to remove damping limitations of the original structure are also possible. The purpose of the procedure is similar to that of using the Guyan or similar model order reduction techniques. However, in our method we do not perform a true model order reduction in the traditional sense. Furthermore, additional gains, which we do not explore herein, can be obtained through the combination of this method with traditional model-order reduction procedures. In our procedure we use the information of the whole system of equations is used but only those nodes of interest to the analyst are processed. That interest comes from the need to obtain the response of the structure at specific locations or from the need to modify the structure at some suitable positions in order to change its behaviour (acceleration, velocity or displacement response) under dynamic loads. Therefore, the procedure is particularly suitable for parametric optimization in large structures with >100000 normal modes such as position of new elements, stiffness, mass and viscous dampings in previous studies where different solutions are devised and optimized, and in the case of large structures, can carry an extremely high number of simulations to get the optimum solution. After the introduction of the required tools and the development of the procedure, a study case is proposed with use the finite element model (FEM) of the MILANO UAV developed by Instituto Nacional de Técnica Aeroespacial. Due to an equipment addition, certain acceleration and displacement requirements on left wing tip and right wing tip, respectively, are imposed. The structure is under a continuous sinusoidal wind gust which produces lift. The proposed modification consists of the addition of an equipment in left wing tip clamped through a rigid attachment or through a dynamic response reduction system with variable properties of mass, stiffness and damping. The analysis of the obtained results allows us to determine the optimized parametric by means of multiple dynamic analyses in a way such that the imposed requirements have been accomplished in the best possible way. The results achieved are compared with results from a commercial finite element analysis software, showing a good correlation. Influence of several factors such as the modal damping of the original structure, the number of modes kept in the modal truncation or the precission given by the frequency sweep is analyzed. Finally, the efficiency of the proposed method is addressed in tems of computational time and data size compared with other approaches. From the analyses performed, we can conclude that the proposed method is a useful and efficient option to perform parametric analysis of possible local modifications in large structures.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

Fatiga en CFRP: Caracterización y Método Óptico para la Estimación del Daño

El desarrollo de nuevas estructuras aeroespaciales optimizadas, utilizan materiales compuestos, para los componentes críticos y subsistemas, principalmente polímeros reforzados con fibra de carbono (CFRP). Un conocimiento profundo del estado de daño por fatiga de estructuras de CFRP avanzado, es esencial para predecir la vida residual y optimizar los intervalos de inspección estructural, reparaciones y/o sustitución de componentes. Las técnicas actuales se basan principalmente en la medición de cargas estructurales a lo largo de la vida útil de la estructura mediante galgas extensométricas eléctricas. Con esos datos, se estima la vida a fatiga utilizando modelos de acumulación de daño. En la presente tesis, se evalúa la metodología convencional para la estimación de la vida a fatiga de un CFRP aeronáutico. Esta metodología está basada en la regla de acumulación de daño lineal de Palmgren-Miner, y es aplicada para determinar la vida a fatiga de estructuras sometidas a cargas de amplitud variable. Se ha realizado una campaña de ensayos con cargas de amplitud constante para caracterizar un CFRP aeronáutico a fatiga, obteniendo las curvas clásicas S-N, en diferentes relaciones de esfuerzo. Se determinaron los diagramas de vida constante, (CLD), también conocidos como diagramas de Goodman, utilizando redes neuronales artificiales debido a la ausencia de modelos coherentes para materiales compuestos. Se ha caracterizado la degradación de la rigidez debido al daño por fatiga. Se ha ensayado un segundo grupo de probetas con secuencias estandarizadas de cargas de amplitud variable, para obtener la vida a fatiga y la degradación de rigidez en condiciones realistas. Las cargas aplicadas son representativas de misiones de aviones de combate (Falstaff), y de aviones de transporte (Twist). La vida a fatiga de las probetas cicladas con cargas de amplitud variable, se comparó con el índice de daño teórico calculado en base a la regla de acumulación de daño lineal convencional. Los resultados obtenidos muestran predicciones no conservativas. Esta tesis también presenta el estudio y desarrollo, de una nueva técnica de no contacto para evaluar el estado de daño por fatiga de estructuras de CFRP por medio de cambios de los parámetros de rugosidad. La rugosidad superficial se puede medir fácilmente en campo con métodos sin contacto, mediante técnicas ópticas tales como speckle y perfilómetros ópticos. En el presente estudio, se han medido parámetros de rugosidad superficial, y el factor de irregularidad de la superficie, a lo largo de la vida de las probetas cicladas con cargas de amplitud constante y variable, Se ha obtenido una buena tendencia de ajuste al correlacionar la magnitud de la rugosidad y el factor de irregularidad de la superficie con la degradación de la rigidez de las probetas fatigadas. Estos resultados sugieren que los cambios en la rugosidad superficial medida en zonas estratégicas de componentes y estructuras hechas de CFRP, podrían ser indicativas del nivel de daño interno debido a cargas de fatiga. Los resultados también sugieren que el método es independiente del tipo de carga de fatiga que ha causado el daño. Esto último hace que esta técnica de medición sea aplicable como inspección para una amplia gama de estructuras de materiales compuestos, desde tanques presurizados con cargas de amplitud constante, estructuras aeronáuticas como alas y colas de aeronaves cicladas con cargas de amplitud variable, hasta aplicaciones industriales como automoción, entre otros. ABSTRACT New optimized aerospace structures use composite materials, mainly carbon fiber reinforced polymer composite (CFRP), for critical components and subsystems. A strong knowledge of the fatigue state of highly advanced (CFRP) structures is essential to predict the residual life and optimize intervals of structural inspection, repairs, and/or replacements. Current techniques are based mostly on measurement of structural loads throughout the service life by electric strain gauge sensors. These sensors are affected by extreme environmental conditions and by fatigue loads in such a way that the sensors and their systems require exhaustive maintenance throughout system life. In the present thesis, the conventional methodology based on linear damage accumulation rules, applied to determine the fatigue life of structures subjected to variable amplitude loads was evaluated for an aeronautical CFRP. A test program with constant amplitude loads has been performed to obtain the classical S-N curves at different stress ratios. Constant life diagrams, CLDs, where determined by means of Artificial Neural Networks due to the absence of consistent models for composites. The stiffness degradation due to fatigue damage has been characterized for coupons under cyclic tensile loads. A second group of coupons have been tested until failure with a standardized sequence of variable amplitude loads, representative of missions for combat aircraft (Falstaff), and representative of commercial flights (Twist), to obtain the fatigue life and the stiffness degradation under realistic conditions. The fatigue life of the coupons cycled with variable amplitude loads were compared to the theoretical damage index calculated based on the conventional linear damage accumulation rule. The obtained results show non-conservative predictions. This thesis also presents the evaluation of a new non-contact technique to evaluate the fatigue damage state of CFRP structures by means of measuring roughness parameters to evaluate changes in the surface topography. Surface roughness can be measured easily on field with non-contact methods by optical techniques such as speckle and optical perfilometers. In the present study, surface roughness parameters, and the surface irregularity factor, have been measured along the life of the coupons cycled with constant and variable amplitude loads of different magnitude. A good agreement has been obtained when correlating the magnitude of the roughness and the surface irregularity factor with the stiffness degradation. These results suggest that the changes on the surface roughness measured in strategic zones of components and structures made of CFRP, could be indicative of the level of internal damage due to fatigue loads. The results also suggest that the method is independent of the type of fatigue load that have caused the damage. It makes this measurement technique applicable for a wide range of inspections of composite materials structures, from pressurized tanks with constant amplitude loads, to variable amplitude loaded aeronautical structures like wings and empennages, up to automotive and other industrial applications.

Optimización del multiplex de televisión

Este proyecto versa sobre un modelo de evaluación de calidad de imagen aplicado a la optimización del ancho de banda del multiplex de televisión, mediante la realización de ensayos con distintas configuraciones de cabecera. Dicho modelo se basa en las medidas PQR y DMOS de Tektronix, destinadas a medir la percepción de las diferencias entre una secuencia antes y después de sufrir un procesado digital. Dado que actualmente, el modo de trabajo de una cabecera de televisión digital, es la multiplexación estadística (consistente en la codificación de diferentes servicios de vídeo con anchos de banda variables en función de la complejidad de las señales), las medidas estarán enfocadas a sacar conclusiones acerca de la cantidad de canales, complejidad de contenidos, y organización de los mismos en el ancho de banda disponible para emitir, manteniendo niveles de calidad Broadcast. Las medidas serán aplicadas en el proyecto para comparar el rendimiento de dos modelos de cabecera. En primer lugar serán configuradas en régimen binario constante, comparando el rendimiento de los codificadores en el área de trabajo habitual. Posteriormente se configuraran en régimen binario variable probando múltiples configuraciones, con el objetivo dar con el modelo y configuración óptima para su posterior implementación. ABSTRACT. This project concerns a picture quality assessment model applied to television multiplex bandwidth optimization by conducting test with different headend settings. This model is based on the PQR and DMOS Tektronix measures, designed to measure the differences between a sequence before and after a digital processing. Given that nowadays the working way of television headend is by statistical multiplexing (based on coding the different video services with variable bitrate depending on the complexity of the signals) measures will be focused to reach conclusions about the number of channels, complexity of content, and the way to organize them through the available bandwidth, keeping broadcast quality ratios. The measures will be applied comparing the performance of two headend models. First of all encoders will be set on constant bitrate, comparing the performance through the working bandwidth. Later on, both models will be set on variable bitrate testing multiple configurations, in order to find the optimal model/configuration for later implementation.

Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: Implications for retroviral assembly mechanisms

We have used electron cryo-microscopy and image analysis to examine the native structure of immature, protease-deficient (PR−) and mature, wild-type (WT) Moloney murine leukemia virus (MuLV). Maturational cleavage of the Gag polyprotein by the viral protease is associated with striking morphological changes. The PR− MuLV particles exhibit a rounded central core, which has a characteristic track-like shell on its surface, whereas the WT MuLV cores display a polygonal surface with loss of the track-like feature. The pleomorphic shape and inability to refine unique orientation angles suggest that neither the PR− nor the WT MuLV adheres to strict icosahedral symmetry. Nevertheless, the PR− MuLV particles do exhibit paracrystalline order with a spacing between Gag molecules of ≈45 Å and a length of ≈200 Å. Because of the pleomorphic shape and paracrystalline packing of the Gag–RNA complexes, we raise the possibility that assembly of MuLV is driven by protein–RNA, as well as protein–protein, interactions. The maturation process involves a dramatic reorganization of the packing arrangements within the ribonucleoprotein core with disordering and loosening of the individual protein components.

DNA packing in stable lipid complexes designed for gene transfer imitates DNA compaction in bacteriophage

The structure of complexes made from DNA and suitable lipids (lipoplex, Lx) was examined by cryo-electron microscopy (cryoEM). We observed a distinct concentric ring-like pattern with striated shells when using plasmid DNA. These spherical multilamellar particles have a mean diameter of 254 nm with repetitive spacing of 7.5 nm with striation of 5.3 nm width. Small angle x-ray scattering revealed repetitive ordering of 6.9 nm, suggesting a lamellar structure containing at least 12 layers. This concentric and lamellar structure with different packing regimes also was observed by cryoEM when using linear double-stranded DNA, single-stranded DNA, and oligodeoxynucleotides. DNA chains could be visualized in DNA/lipid complexes. Such specific supramolecular organization is the result of thermodynamic forces, which cause compaction to occur through concentric winding of DNA in a liquid crystalline phase. CryoEM examination of T4 phage DNA packed either in T4 capsides or in lipidic particles showed similar patterns. Small angle x-ray scattering suggested an hexagonal phase in Lx-T4 DNA. Our results indicate that both lamellar and hexagonal phases may coexist in the same Lx preparation or particle and that transition between both phases may depend on equilibrium influenced by type and length of the DNA used.

Peptides containing glutamine repeats as substrates for transglutaminase-catalyzed cross-linking: Relevance to diseases of the nervous system

Many proteins contain reiterated glutamine residues, but polyglutamine of excessive length may result in human disease by conferring new properties on the protein containing it. One established property of a glutamine residue, depending on the nature of the flanking residues, is its ability to act as an amine acceptor in a transglutaminase-catalyzed reaction and to make a glutamyl–lysine cross-link with a neighboring polypeptide. To learn whether glutamine repeats can act as amine acceptors, we have made peptides with variable lengths of polyglutamine flanked by the adjacent amino acid residues in the proteins associated with spinocerebellar ataxia type 1 (SCA1), Machado–Joseph disease (SCA3), or dentato-rubral pallido-luysian atrophy (DRPLA) or those residues adjacent to the preferred cross-linking site of involucrin, or solely by arginine residues. The polyglutamine was found to confer excellent substrate properties on any soluble peptide; under optimal conditions, virtually all the glutamine residues acted as amine acceptors in the reaction with glycine ethyl-ester, and lengthening the sequence of polyglutamine increased the reactivity of each glutamine residue. In the presence of transglutaminase, peptides containing polyglutamine formed insoluble aggregates with the proteins of brain extracts and these aggregates contained glutamyl–lysine cross-links. Repeated glutamine residues exposed on the surface of a neuronal protein should form cross-linked aggregates in the presence of any transglutaminase activated by the presence of Ca2+.

Ligand-dependent activation of transcription in vitro by retinoic acid receptor α/retinoid X receptor α heterodimers that mimics transactivation by retinoids in vivo

All-trans and 9-cis retinoic acids (RA) signals are transduced by retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers that act as functional units controlling the transcription of RA-responsive genes. With the aim of elucidating the underlying molecular mechanisms, we have developed an in vitro transcription system using a chromatin template made up of a minimal promoter and a direct repeat with 5-spacing-based RA response element. RARα and RXRα were expressed in and purified from baculovirus-infected Sf9 cells, and transcription was carried out by using naked DNA or chromatin templates. Transcription from naked templates was not affected by the presence of RA and/or RAR/RXR heterodimers. In contrast, very little transcription occurred from chromatin templates in the absence of RA or RAR/RXR heterodimers whereas their addition resulted in a dosage-dependent stimulation of transcription that never exceeded that occurring on naked DNA templates. Most importantly, the addition of synthetic agonistic or antagonistic retinoids to the chromatin transcription system mimicked their stimulatory or inhibitory action in vivo, and activation by a RXR-specific retinoid was subordinated to the binding of an agonist ligand to the RAR partner. Moreover, the addition of the p300 coactivator generated a synergistic enhancement of transcription. Thus, the dissection of this transcription system ultimately should lead to the elucidation of the molecular mechanisms by which RAR/RXR heterodimers control transcription in a ligand-dependent manner.

Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene

The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternative splicing, minigenes of TPO genomic constructs with variable exon–intron configurations or carrying exclusively the TPO cDNA were generated and transiently transfected in the Hep3B cell line. We have found that the final rate of the alternative intron splicing is determined by three elements: the presence of upstream constitutive introns, the suboptimal splice sites of the alternative intron and the length of the alternative intron itself. Our results indicate that the recognition of suboptimal intra-exonic splice junctions in the TPO gene is influenced by the assembly of the spliceosome complex on constitutive introns and by a qualitative scanning of the sequence by the transcriptional/splicing machinery complex primed by upstream splicing signals.

Morphology of high-luminosity compact radio sources.

High-dynamic range imaging and monitoring with very-long-baseline interferometry reveal a rich morphology of luminous flat-spectrum radio sources. One-sided core-jet structures abound, and superluminal motion is frequently measured. In a few cases, both distinct moving features and diffuse underlying jet emission can be detected. Superluminal motion seen in such sources is typically complex, on curved trajectories or ridge lines, and with variable component velocities, including stationary features. The curved trajectories seen can be modeled by helical motion within the underlying jet flow. The very-long-baseline interferometry properties of the superluminal features in the jet of 3C 345 and other similar sources can be explained by models invoking the emission from shocks, at least within the vicinity of the compact core. Inverse-Compton calculations, constrained by x-ray observations, yield realistic estimates for the physical conditions in the parsec-scale jet. There is evidence for a transition region in this source beyond which other factors (e.g., plasma interactions and nonsynchrotron radiation processes) may become prominent. Multifrequency and polarization imaging (especially at high frequencies) are emerging as critical tools in testing model predictions.

The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element.

Alu repeats are interspersed repetitive DNA elements specific to primates that are present in 500,000 to 1 million copies. We show here that an Alu sequence encodes functional binding sites for retinoic acid receptors, which are members of the nuclear receptor family of transcription factors. The consensus sequences for the evolutionarily recent Alu subclasses contain three hexamer half sites, related to the consensus AGGTCA, arranged as direct repeats with a spacing of 2 bp, which is consistent with the binding specificities of retinoic acid receptors. An analysis was made of the DNA binding and transactivation potential of these sites from an Alu sequence that has been previously implicated in the regulation of the keratin K18 gene. These Alu double half sites are shown to bind bacterially synthesized retinoic acid receptors as assayed by electrophoretic mobility shift assays. These sites are further shown to function as a retinoic acid response element in transiently transfected CV-1 cells, increasing transcription of a reporter gene by a factor of approximately 35-fold. This transactivation requires cotransfection with vectors expressing retinoic acid receptors, as well as the presence of all-trans-retinoic acid, which is consistent with the known function of retinoic acid receptors as ligand-inducible transcription factors. The random insertion of potentially thousands of Alu repeats containing retinoic acid response elements throughout the primate genome is likely to have altered the expression of numerous genes, thereby contributing to evolutionary potential.

TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a toroid-shaped molecule that binds transcripts containing GAG or UAG repeats separated by two nucleotides.

The trp RNA-binding attenuation protein of Bacillus subtilis, TRAP, regulates both transcription and translation by binding to specific transcript sequences. The optimal transcript sequences required for TRAP binding were determined by measuring complex formation between purified TRAP protein and synthetic RNAs. RNAs were tested that contained repeats of different trinucleotide sequences, with differing spacing between the repeats. A transcript containing GAG repeats separated by two-nucleotide spacers was bound most tightly. In addition, transmission electron microscopy was used to examine the structure of TRAP and the TRAP-transcript complex. TRAP was observed to be a toroid-shaped oligomer when free or when bound to either a natural or a synthetic RNA.

Founder-effect speciation theory: failure of experimental corroboration.

The theory of founder-effect speciation proposes that colonization by very few individuals of an empty habitat favors rapid genetic changes and the evolution of a new species. We report here the results obtained in a 10-year-long and large-scale experiment with Drosophila pseudoobscura designed to test the theory. In our experimental protocol, populations are established with variable numbers of very few individuals and allowed to expand greatly for several generations until conditions of severe competition for resources are reached and the population crashes. A few random survivors are then taken to start a new population expansion and thus initiate a new cycle of founding events, population flushes, and crashes. Our results provide no support for the theories proposing that new species are very likely to appear as by-products of founder events.

Caracterização de rearranjos cromossômicos citogeneticamente equilibrados associados a quadros clínicos

Este estudo teve como objetivos (a) identificar mecanismos pelos quais rearranjos cromossômicos citogeneticamente equilibrados possam estar associados de maneira causal a determinados quadros clínicos e (b) contribuir para a compreensão dos mecanismos de formação desses rearranjos. Para isso, foram estudados 45 rearranjos cromossômicos citogeneticamente equilibrados (29 translocações, 10 inversões e seis rearranjos complexos), detectados em pacientes que apresentavam malformações congênitas, comprometimento do desenvolvimento neuropsicomotor ou déficit intelectual. Foram 31 rearranjos cromossômicos esporádicos, três familiais que segregavam com o quadro clínico e mais 11 rearranjos cromossômicos herdados de genitores fenotipicamente normais. Inicialmente os pontos de quebra desses rearranjos foram mapeados por hibridação in situ fluorescente (FISH). A busca por microdeleções e duplicações genômicas foi realizada por a-CGH. A investigação dos pontos de quebra prosseguiu com a aplicação da técnica de Mate-Pair Sequencing (MPS), que permite localizar as quebras em segmentos de 100 pb - 1 kb, na maioria dos casos. Para obter os segmentos de junção das quebras no nível de pares de bases, os segmentos delimitados por MPS foram sequenciados pelo método de Sanger. A análise por aCGH revelou microdeleções ou microduplicações localizadas nos cromossomos rearranjados, em 12 dos 45 pacientes investigados (27%). A análise de 27 rearranjos por MPS permitiu a caracterização dos pontos de junção das quebras. MPS expandiu o número de pontos de quebra, detectados por análise do cariótipo ou aCGH, de 114 para 156 (em resolução < 2kb, na maioria dos casos). O número de pontos de quebra/rearranjo variou de 2 a 20. Os 156 pontos de quebra resultaram em 86 variantes estruturais equilibradas e outras 32 variantes não equilibradas. Perdas e ganhos de segmentos submiscroscópicos nos cromossomos rearranjados constituíram a principal causa ou, provavelmente, contribuíram para o quadro clínico de 12 dos 45 pacientes. Em cinco desses 12 rearranjos foram detectadas por MPS a interrupção de genes já relacionados à doença, ou provável alteração de sua região reguladora, contribundo para o quadro clínico. Em quatro dos 33 rearranjos não associados a perdas ou ganhos de segmentos, a análise por MPS revelou a interrupção de genes que já foram anteriormente relacionados a doenças, explicando-se, assim, as características clínicas dos portadores; outro rearranjo pode ter levando alteração da expressão gênica de gene sensível a dosagem e ao quadro clínico. Um rearranjo cromossômico familial, identificado na análise após bandamento G como uma translocação equilibrada, t(2;22)(p14;q12), segregava com quadro de atraso do desenvolvimento neuropsicomotor e dificuldade de aprendizado associados a dismorfismos. A combinação das análises por FISH, aCGH e MPS revelou que se tratava, na verdade, de rearranjo complexo entre os cromossomos 2, 5 e 22, incluindo 10 quebras. A segregação de diferentes desequilíbrios submicroscópicos em indivíduos afetados e clinicamente normais permitiu a compreensão da variabilidade clínica observada na família. Rearranjos equilibrados detectados em indivíduos afetados, mas herdados de genitores clinicamente normais, são, em geral, considerados como não tendo relação com o quadro clínico, apesar da possibilidade de desequilíbrios cromossômicos gerados por permuta desigual na meiose do genitor portador do rearranjo. Neste trabalho, a investigação de 11 desses rearranjos por aCGH não revelou perdas ou ganhos de segmentos nos cromossomos rearranjados. No entanto, a análise por aCGH da portadora de um desses rearranjos - inv(12)mat - revelou deleção de 8,7 Mb no cromossomo 8, como causa de seu fenótipo clínico. Essa deleção estava relacionada com outro rearranjo equilibrado também presente em sua mãe, independente da inversão. Para compreender os mecanismos de formação de rearranjos citogeneticamente equilibrados, investigamos os segmentos de junção no nível de pares de base. A análise por MPS que levou, na maioria dos casos, ao mapeamento dos pontos de quebras em segmentos <1kb permitiu o sequenciamento pelo método de Sanger de 51 segmentos de junções de 17 rearranjos. A ocorrência de blunt fusions ou inserções e deleções <10 pb, e a ausência de homologia ou a presença de micro homologia de 2 pb a 4 pb de extensão indicaram o mecanismo de junção de extremidades não homólogas (non-homologous end joinging; NHEJ), na maioria das 51 junções caracterizadas. As características de três dos quatro rearranjos mais complexos, com 17-20 quebras, indicaram sua formação pelo mecanismo de chromothripsis. Este estudo mostra a importância da análise genômica de variações de número de cópias por microarray, juntamente com o mapeamento dos pontos de quebra por MPS, para determinar a estrutura de rearranjos cromossômicos citogeneticamente equilibrados e seu impacto clínico. O mapeamento dos segmentos de junção por MPS, permitindo o sequenciamento pelo método de Sanger, foi essencial para a compreensão de mecanismos de formação desses rearranjos