Database on the molluscan fauna from the Mediterranean Reef Ecosystems (CorMolDB - Part I)

In the Mediterranean Sea, infralittoral and circalittoral rocky bottoms (from 15 to 120 m) are characterized by a biogenic habitat, named "coralligenous", formed by the concretion of calcareous organisms, mainly algal thalli, and- to a lesser extent- by animal skeletons. This complex habitat is inhabited by a rich fauna that belongs to different taxonomic groups. Sponges, bryozoans, cnidarians and ascidians are the most common sessile organisms that inhabit the area while crustacean and molluscs are the common mobile organisms. Little information on the diversity of the molluscs that thrive in the coralligenous habitat is known while this information is highly important for biodiversity management purposes. After thoroughly studying the available and accessible published literature, a database for the molluscs of the coralligenous habitat has been designed and implemented for the collection and management of this information. From its index compilation more than 511 species of molluscs have been recorded so far from the coralligenous formations, the majority of which belongs to the class Gastropoda (357 sp.) followed by the Bivalvia (137 sp.), Polyplacophora (14 sp.), Cephalopoda (2 sp.) and Scaphopoda (1 sp.). Among these, the gastropod Luria lurida (Linnaeus, 1758) and Charonia lampas (Linnaeus, 1758), the endemic bivalve Pinna nobilis Linnaeus, 1758 and the endolithic bivalve Lithophaga lithophaga (Linnaeus, 1758), are protected by international conventions.

Hydration of C3S, C2S and their Blends. Micro- and Nanoscale Characterization

This study forms part of wider research conducted under a EU 7 th Framework Programme (COmputationally Driven design of Innovative CEment-based materials or CODICE). The ultimate aim is the multi-scale modelling of the variations in mechanical performance in degraded and non-degraded cementitious matrices. The model is being experimentally validated by hydrating the main tri-calcium silicate (T1-C3S) and bi-calcium silicate (β-C2S), phases present in Portland cement and their blends. The present paper discusses micro- and nanoscale studies of the cementitious skeletons forming during the hydration of C3S, C2S and 70 % / 30 % blends of both C3S/C2S and C2S/C3S with a water/cement ratio of 0.4. The hydrated pastes were characterized at different curing ages with 29 Si NMR, SEM/TEM/EDS, BET, and nanoindentation. The findings served as a basis for the micro- and nanoscale characterization of the hydration products formed, especially C-S-H gels. Differences were identified in composition, structure and mechanical behaviour (nanoindentation), depending on whether the gels formed in C3S or C2S pastes. The C3S gels had more compact morphologies, smaller BET-N2 specific surface area and lesser porosity than the gels from C2S-rich pastes. The results of nanoindentation tests appear to indicate that the various C-S-H phases formed in hydrated C3S and C2S have the same mechanical properties as those formed in Portland cement paste. Compared to the C3S sample, the hydrated C2S specimen was dominated by the loose-packed (LP) and the low-density (LD) C-S-H phases, and had a much lower content of the high density (HD) C-S-H phase

Mapping of mechanical properties of cement paste microstructures

The presented study is related to the EU 7 th Framework Programme CODICE (COmputationally Driven design of Innovative CEment-based materials). The main aim of the project is the development of a multi-scale model for the computer based simulation of mechanical and durability performance of cementitious materials. This paper reports results of micro/nano scale characterisation and mechanical property mapping of cementitious skeletons formed by the cement hydration at different ages. Using the statistical nanoindentation and micro-mechanical property mapping technique, intrinsic properties of different hydrate phases, and also the possible interaction (or overlapping) of different phases (e.g. calcium-silcate-hydrates) has been studied. Results of the mapping and statistical indentation testing appear to suggest the possible existence of more hydrate phases than the commonly reported LD and HD C-S-H and CH phases

Behaviour Driven Development for Multi-Agent Systems

This paper presents a testing methodology to apply Behaviour Driven Development (BDD) techniques while developing Multi-Agent Systems (MAS), so called BEhavioural Agent Simple Testing (BEAST) methodology. It is supported by the developed open source framework (BEAST Tool) which automatically generates test cases skeletons from BDD scenarios specifications. The developed framework allows testing MASs based on JADE or JADEX platforms and offers a set of configurable Mock Agents which allow the execution of tests while the system is under development. BEAST tool has been validated in the development of a MAS for fault diagnosis in FTTH (Fiber To The Home) networks.

Arrecifes de corales de aguas frías como posibles indicadores de emisiones de hidrocarburos en el Golfo de Cádiz

El presente documento trata de exponer la relación existente entre los corales de aguas frías encontrados en el Golfo de Cádiz (Atlántico NE) con los procesos tectónicos y las estructuras relacionadas con la migración y la emisión de fluidos ricos en hidrocarburos (principalmente metano). Para ello, desde el año 2000 hasta la actualidad, se han llevado a cabo diversas campañas oceanográficas en las cuales se han obtenido datos y muestras relacionadas con las emisiones de hidrocarburos al fondo marino. Gracias a los datos y las muestras recogidas durante las campañas se han creado una base de datos, en la que se reúnen todos los datos significativos relacionados con las campañas oceanográficas y con el objeto de este trabajo. Para finalizar, tras la creación de la base de datos, y con las muestras proporcionadas por el IGME recogidas durante la campaña oceanográfica MVSEIS08, se han podido llevar a cabo diversos estudios de laboratorio como la racemización de aminoácidos, análisis de biomarcadores así como la datación de los esqueletos aragoníticos de los corales de aguas frías mediante la técnica de U-Th en un futuro, con el objetivo de esclarecer la relación existente entre estas emisiones de fluidos a través de diversas estructuras y los corales de aguas frías, su edad, y en última instancia determinar los cambios producidos en la composición química de la masa de agua atlántica así como la variación de las corrientes en el Golfo de Cádiz durante el último periodo glaciar. ABSTRACT This project attempts to explain the relationship between cold-water coral found in the Gulf of Cadiz (NE Atlantic) with tectonic processes and structures related to migration and hydrocarbon-rich fluids emissions (mainly methane). Since 2000 until present, have conducted various oceanographic cruises in which data were obtained and samples related to hydrocarbon emissions to the seabed. Thanks to data and samples collected during the cruises, I have created a database in which all gather meaningful data related to oceanographic and the object of this work. Finally, after the creation of the database, and the samples provided by the IGME collected during the oceanographic cruise MVSEIS08 have been able to carry out laboratory studies of racemization of aminoacids, biomarkers analysis and dating of aragonitic skeletons of cold-water corals in a future by U-Th data , in order to clarify the relationship between these fluids emissions through various structures, ages cold-water corals, and ultimately determine changes in the chemical composition of Atlantic water mass and the change of currents in the Gulf of Cadiz during the last glacial period.

Posibilidades del motor 3D de la Nintendo DS

La consola portátil Nintendo DS es una plataforma de desarrollo muy presente entre la comunidad de desarrolladores independientes, con una extensa y nutrida escena homebrew. Si bien las capacidades 2D de la consola están muy aprovechadas, dado que la mayor parte de los esfuerzos de los creadores amateur están enfocados en este aspecto, el motor 3D de ésta (el que se encarga de representar en pantalla modelos tridimensionales) no lo está de igual manera. Por lo tanto, en este proyecto se tiene en vista determinar las capacidades gráficas de la Nintendo DS. Para ello se ha realizado una biblioteca de funciones en C que permite aprovechar las posibilidades que ofrece la consola en el terreno 3D y que sirve como herramienta para la comunidad homebrew para crear aplicaciones 3D de forma sencilla, dado que se ha diseñado como un sistema modular y accesible. En cuanto al proceso de renderizado se han sacado varias conclusiones. En primer lugar se ha determinado la posibilidad de asignar varias componentes de color a un mismo vértice (color material reactivo a la iluminación, color por vértice directo y color de textura), tanto de forma independiente como simultáneamente, pudiéndose utilizar para aplicar diversos efectos al modelo, como iluminación pre-calculada o simulación de una textura mediante color por vértice, ahorrando en memoria de video. Por otro lado se ha implementado un sistema de renderizado multi-capa, que permite realizar varias pasadas de render, pudiendo, de esta forma, aplicar al modelo una segunda textura mezclada con la principal o realizar un efecto de reflexión esférica. Uno de los principales avances de esta herramienta con respecto a otras existentes se encuentra en el apartado de animación. El renderizador desarrollado permite por un lado animación por transformación, consistente en la animación de mallas o grupos de vértices del modelo mediante el movimiento de una articulación asociada que determina su posición y rotación en cada frame de animación. Por otro lado se ha implementado un sistema de animación por muestreo de vértices mediante el cual se determina la posición de éstos en cada instante de la animación, generando frame a frame las poses que componen el movimiento (siendo este último método necesario cuando no se puede animar una malla por transformación). Un mismo modelo puede contener diferentes esqueletos, animados independientemente entre sí, y cada uno de ellos tener definidas varias costumbres de animación que correspondan a movimientos contextuales diferentes (andar, correr, saltar, etc). Además, el sistema permite extraer cualquier articulación para asociar su transformación a un objeto estático externo y que éste siga el movimiento de la animación, pudiendo así, por ejemplo, equipar un objeto en la mano de un personaje. Finalmente se han implementado varios efectos útiles en la creación de escenas tridimensionales, como el billboarding (tanto esférico como cilíndrico), que restringe la rotación de un modelo para que éste siempre mire a cámara y así poder emular la apariencia de un objeto tridimensional mediante una imagen plana, ahorrando geometría, o emplearlo para realizar efectos de partículas. Por otra parte se ha implementado un sistema de animación de texturas por subimágenes que permite generar efectos de movimiento mediante imágenes, sin necesidad de transformar geometría. ABSTRACT. The Nintendo DS portable console has received great interest within the independent developers’ community, with a huge homebrew scene. The 2D capabilities of this console are well known and used since most efforts of the amateur creators has been focused on this point. However its 3D engine (which handles with the representation of three-dimensional models) is not equally used. Therefore, in this project the main objective is to assess the Nintendo DS graphic capabilities. For this purpose, a library of functions in C programming language has been coded. This library allows the programmer to take advantage of the possibilities that the 3D area brings. This way the library can be used by the homebrew community as a tool to create 3D applications in an easy way, since it has been designed as a modular and accessible system. Regarding the render process, some conclusions have been drawn. First, it is possible to assign several colour components to the same vertex (material colour, reactive to the illumination, colour per vertex and texture colour), independently and simultaneously. This feature can be useful to apply certain effects on the model, such as pre-calculated illumination or the simulation of a texture using colour per vertex, providing video memory saving. Moreover, a multi-layer render system has been implemented. This system allows the programmer to issue several render passes on the same model. This new feature brings the possibility to apply to the model a second texture blended with the main one or simulate a spherical reflection effect. One of the main advances of this tool over existing ones consists of its animation system. The developed renderer includes, on the one hand, transform animation, which consists on animating a mesh or groups of vertices of the model by the movement of an associated joint. This joint determines position and rotation of the mesh at each frame of the animation. On the other hand, this tool also implements an animation system by vertex sampling, where the position of vertices is determined at every instant of the animation, generating the poses that build up the movement (the latter method is mandatory when a mesh cannot be animated by transform). A model can contain multiple skeletons, animated independently, each of them being defined with several animation customs, corresponding to different contextual movements (walk, run, jump, etc). Besides, the system allows extraction of information from any joint in order to associate its transform to a static external object, which will follow the movement of the animation. This way, any object could be equipped, for example, on the hand of a character. Finally, some useful effects for the creation of three-dimensional scenes have been implemented. These effects include billboarding (both spherical and cylindrical), which constraints the rotation of a model so it always looks on the camera's direction. This feature can provide the ability to emulate the appearance of a three-dimensional model through a flat image (saving geometry). It can also be helpful in the implementation of particle effects. Moreover, a texture animation system using sub-images has also been implemented. This system allows the generation of movement by using images as textures, without having to transform geometry.

Arrecifes de corales de aguas frías como posibles indicadores de emisiones de hidrocarburos en el banco de Galicia y determinación de su edad mediante racemizacion de aminoácidos

Este proyecto tiene como objetivo analizar la posible relación entre los corales de aguas frías encontrados en el Banco de Galicia con los procesos tectónicos y las estructuras relacionadas con la migración y la emisión de fluidos ricos en hidrocarburos (debido a su interés económico), así como la creación de un algoritmo que establezca una relación entre el grado de racemización sufrido por los aminoácidos de las muestras y la edad de estas. Para ello, se han recopilado datos y muestras en el área de estudio, gracias a los cuales se ha creado una base de datos que contiene una clasificación de las muestras recogidas junto a los datos más relevantes de que están relacionados con el objetivo de este trabajo. Estas muestras han sido proporcionadas por el IGME y fueron recogidas mayoritariamente en la campaña oceanográfica DIVA ARTABRIA II. Con estas muestras se han llevado a cabo análisis de laboratorio como el estudio de racemización de aminoácidos, el análisis de biomarcadores y la datación por uranio-torio de los esqueletos aragoníticos de los corales de aguas frías. Para finalizar, se han estudiado dichos datos con el objeto de comprobar la hipótesis de que los corales de aguas frías colonizan zonas con emisiones de hidrocarburos, conocer su edad y en última instancia crear un algoritmo capaz de datar dichos corales a partir del grado de racemización de sus aminoácidos. Palabras clave: corales de aguas frías, Banco de Galicia, campaña oceanográfica, DIVA ARTABRIA II, base de datos, racemización, aminoácidos, biomarcadores, datación uranio-torio, hidrocarburos, algoritmo. ABSTRACT This project studies the relationship between cold-water corals found in the Galicia Bank with tectonic processes and with the structures related to migration and hydrocarbon-rich fluids emissions. Firstly, data and samples in the study were collected, through to classify the collected samples with the most relevant characteristics to our research scope. Sampling and data collection provided by the IGME were collected in the DIVA ARTABRIA II oceanographic cruise. Secondly, the current work presents a systematic laboratory analysis that allowed the study of aminoacid racemization as well as the analysis of biomarkers and the uranium-thorium dating of aragonitic cold-water coral skeletons. Finally, this data was studied to test the hypothesis that cold-water corals colonize areas with emissions of hydrocarbons, know its age and ultimately create and algorithm capable of dating these corals from the degree of racemization in its amino acids. Keywords: cold-water corals, Galicia Bank, oceanographic cruise, DIVA ARTABRIA II, database, racemization, amino acids, biomarkers, uranium-thorium datation, hydrocarbons, algorithm.

Sistemas radiolarios: geometrías y arquitecturas derivadas

Uno de los temas más importantes dentro del debate contemporáneo, es el que se refiere a la sostenibilidad a largo plazo de la sociedad tal y como la entendemos hoy. El ser humano está recuperando la sensibilidad perdida que le concebía como una pieza más dentro del ciclo natural de la vida. Por fin hemos entendido que no podemos ser auto suficientes e independientes del entorno natural que nos rodea. Más allá del respeto y del cuidado, está abierta la puerta del conocimiento infinito que nos brinda la naturaleza a todos los niveles y a todas las escalas. Dentro de la disciplina arquitectónica han existido ejemplos como Antoni Gaudí o Frei Otto que han referenciado su obra en el mundo Natural, encontrando en él las estrategias y bases para el diseño arquitectónico. Sin embargo han sido una minoría dentro del enorme elenco de arquitectos defensores del ángulo recto. En las últimas décadas, la tendencia está cambiando. No nos referimos tanto a la sensibilidad creciente por conseguir una mayor eficiencia energética que ha llevado a una puesta en valor de la arquitectura vernácula, trasladando su sabiduría a las estrategias bioclimáticas. Nos referimos a un caso específico dentro del amplio abanico de formas arquitectónicas que han aparecido gracias a la incorporación de las herramientas computacionales en el diseño y la producción. Las arquitecturas que nos interesan son las que aprovechan estas técnicas para analizar e interpretar las estrategias complejas y altamente eficientes que encontramos en la naturaleza, y trasladarlas a la disciplina arquitectónica. Esta tendencia que se enmarca dentro de la Biomímesis o Biomimética es conocida con el nombre de Bioarquitectura. La presente tesis trata de morfología y sobre todo de morfogénesis. El término morfología se refiere al estudio de una forma concreta que nos permite entender un caso específico, nuestro foco de atención se centra sin embargo en la morfogénesis, es decir, en el estudio de los procesos de generación de esas formas, para poder reproducir patrones y generar abanicos de casos adaptables y reconfigurables. El hecho de estudiar la forma no quiere decir que ésta sea una tesis “formalista” con la connotación peyorativa y gestual que se le suele atribuir a este término. La investigación concibe el concepto de forma como lo hace el mundo natural: forma como síntesis de eficiencia. No hay ninguna forma natural gratuita, que no cumpla una función determinada y que no se desarrolle con el mínimo material y gaste la mínima energía posible. Este afán por encontrar la “forma eficaz” es lo que nos hace traspasar la frontera de la arquitectura formalista. El camino de investigación morfológica se traza, como el título de la tesis indica, siguiendo el hilo conductor concreto de los radiolarios. Estos microorganismos unicelulares poseen unos esqueletos tan complejos que para poder entender su morfología es necesario establecer un amplio recorrido que abarca más de 4.000 años de conocimiento humano. Desde el descubrimiento de los sólidos platónicos, poliedros que configuran muchas de las formas globales de estos esqueletos; hasta la aplicación de los algoritmos generativos, que permiten entender y reproducir los patrones de comportamiento que existen detrás de los sistemas de compactación y teselación irregular de los esqueletos radiolarios. La tesis no pretende plantear el problema desde un punto de vista biológico, ni paleontológico, aunque inevitablemente en el primer capítulo se realiza un análisis referenciado del estado del conocimiento científico actual. Sí se analizan en mayor profundidad cuestiones morfológicas y se tratan los diferentes posicionamientos desde los cuales estos microorganismos han servido de referencia en la disciplina arquitectónica. Además encontramos necesario analizar otros patrones naturales que comparten estrategias generativas con los esqueletos radiolarios. Como ya hemos apuntado, en el segundo capítulo se aborda un recorrido desde las geometrías más básicas a las más complejas, que tienen relación con las estrategias de generación de las formas detectadas en los microorganismos. A su vez, el análisis de estas geometrías se intercala con ejemplos de aplicaciones dentro de la arquitectura, el diseño y el arte. Finalizando con un cronograma que sintetiza y relaciona las tres vías de investigación abordadas: natural, geométrica y arquitectónica. Tras los dos capítulos centrales, el capítulo final recapitula las estrategias analizadas y aplica el conocimiento adquirido en la tesis, mediante la realización de diferentes prototipos que abarcan desde el dibujo analítico tradicional, a la fabricación digital y el diseño paramétrico, pasando por modelos analógicos de escayola, barras metálicas, resina, silicona, látex, etc. ABSTRACT One of the most important issues in the contemporary debate, is the one concerning the long-term sustainability of society as we understand it today. The human being is recovering the lost sensitivity that conceived us as part of the natural cycle of life. We have finally understood that we cannot be self-sufficient and independent of the natural environment which surrounds us. Beyond respect and care, we’ll find that the gateway to the infinite knowledge that nature provides us at all levels and at all scales is open. Within the architectural discipline, there have been remarkable examples such as Antoni Gaudí or Frei Otto who have inspired their work in the natural world. Both, found in nature the strategies and basis of their architectural designs. However, they have been a minority within the huge cast of architects defenders of the right angle. In recent decades, the trend is changing. We are not referring to the growing sensitivity in trying to achieve energy efficiency that has led to an enhancement of vernacular architecture, transferring its wisdom to bioclimatic strategies. We refer to a specific case within the wide range of architectural forms that have appeared thanks to the integration of computer tools in both design and production processes. We are interested in architectures that exploit these techniques to analyse and interpret the complex and highly efficient strategies found in nature, and shift them to the discipline of architecture. This trend, which is being implemented in the framework of the Biomimicry or biomimetics, is called Bioarchitecture. This thesis deals with morphology and more specifically with morphogenesis. Morphology is the study of a concrete form that allows us to understand a specific case. However, our focus is centered in morphogenesis or, in other words, the study of the processes of generation of these forms, in order to replicate patterns and generate a range of adaptable and reconfigurable cases. The fact of studying shapes does not mean that this is a “formalistic” thesis with the pejorative connotation that is often attributed to this term. This study conceives the concept of shape as Nature does: as a synthesis of efficiency. There is no meaningless form in nature. Furthermore, forms and shapes in nature play a particular role and are developed with minimum energetic consumption. This quest to find the efficient shape is what makes us go beyond formalistic architecture. The road of morphological investigation is traced, as the title of the thesis suggests, following the thread of radiolaria. These single-cell microorganisms possess very complex skeletons, so to be able to understand their morphology we must establish a wide spectrum which spans throughout more than 4.000 years of human knowledge. From the discovery of the platonic solids, polyhedrons which configure a huge range of global shapes of these skeletons, through the application of generative algorithms which allow us to understand and recreate the behavioral patterns behind the systems of compression and irregular tessellation of the radiolarian skeletons. The thesis does not pretend to lay out the problem from a biological, paleontological standpoint, although inevitably the first chapter is developed through an analysis in reference to the current state of the science. A deeper analysis of morphological aspects and different positionings is taken into account where these microorganisms have served as reference in the architectonic discipline. In addition we find necessary to analyse other natural patterns which share generative strategies with radiolarian skeletons. Aforementioned, in the second chapter an itinerary of the most basic geometries to the more complex ones is addressed. These are related, in this chapter, to the generative strategies of the shapes found in microorganisms. At the same time, the analysis of these geometries is placed among examples of applications inside the fields of architecture, design and the arts. To come to an end, a time chart synthesizes and relates the three investigation paths addressed: natural, geometrical and architectonic. After the two central chapters, the final chapter summarises the strategies analysed and applies the knowledge acquired throughout the thesis. This final chapter is shaped by the realization of different prototypes which range from traditional analytical drawings, to digital fabrication and parametric design, going through plaster analogical models, metal bars, resin, silicone, latex, etc.

Plant terpenoid synthases: Molecular biology and phylogenetic analysis

This review focuses on the monoterpene, sesquiterpene, and diterpene synthases of plant origin that use the corresponding C10, C15, and C20 prenyl diphosphates as substrates to generate the enormous diversity of carbon skeletons characteristic of the terpenoid family of natural products. A description of the enzymology and mechanism of terpenoid cyclization is followed by a discussion of molecular cloning and heterologous expression of terpenoid synthases. Sequence relatedness and phylogenetic reconstruction, based on 33 members of the Tps gene family, are delineated, and comparison of important structural features of these enzymes is provided. The review concludes with an overview of the organization and regulation of terpenoid metabolism, and of the biotechnological applications of terpenoid synthase genes.

Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia

Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague (“plague teeth”) and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human β-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase β-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.

Phylogenetic relationships between the Acantharea and the Polycystinea: A molecular perspective on Haeckel’s Radiolaria

Polycystine radiolaria are among few protistan groups that possess a comprehensive fossil record available for study by micropaleontologists. The Polycystinea and the Acantharea, whose skeletons do not become fossilized, were once members of the class “Radiolaria” (“Radiolaria” sensu lato: Polycystinea, Phaeodarea, and Acantharea) originally proposed by Haeckel but are now included in the superclass Actinopoda. Phylogenetic relationships within this superclass remain largely enigmatic. We investigated the evolutionary relationship of the Acantharea and the Polycystinea to other protists using phylogenetic analyses of 16S-like ribosomal RNA (rRNA) coding regions. We circumvented the need to culture these organisms by collecting and maintaining reproductive stages that contain many copies of their genomic DNA. This strategy facilitated extraction of genomic DNA and its purification from symbiont and prey DNA. Phylogenetic trees inferred from comparisons of 16S-like coding regions do not support a shared history between the Acantharea and the Polycystinea. However, the monophyly of the Acantharea and the separate monophyly of the Polycystinea (Spumellarida) are well supported by our molecular-based trees. The acantharian lineage branches among crown organisms whereas the polycystine lineage diverges before the radiation of the crown groups. We conclude that the Actinopoda does not represent a monophyletic evolutionary assemblage and recommend that this taxonomic designation be discarded.

A widely expressed βIII spectrin associated with Golgi and cytoplasmic vesicles

Spectrin is an important structural component of the plasma membrane skeleton. Heretofore-unidentified isoforms of spectrin also associate with Golgi and other organelles. We have discovered another member of the β-spectrin gene family by homology searches of the GenBank databases and by 5′ rapid amplification of cDNA ends of human brain cDNAs. Collectively, 7,938 nucleotides of contiguous clones are predicted to encode a 271,294-Da protein, called βIII spectrin, with conserved actin-, protein 4.1-, and ankyrin-binding domains, membrane association domains 1 and 2, a spectrin dimer self-association site, and a pleckstrin-homology domain. βIII spectrin transcripts are concentrated in the brain and present in the kidneys, liver, and testes and the prostate, pituitary, adrenal, and salivary glands. All of the tested tissues contain major 9.0-kb and minor 11.3-kb transcripts. The human βIII spectrin gene (SPTBN2) maps to chromosome 11q13 and the mouse gene (Spnb3) maps to a syntenic region close to the centromere on chromosome 19. Indirect immunofluorescence studies of cultured cells using antisera specific to human βIII spectrin reveal a Golgi-associated and punctate cytoplasmic vesicle-like distribution, suggesting that βIII spectrin associates with intracellular organelles. This distribution overlaps that of several Golgi and vesicle markers, including mannosidase II, p58, trans-Golgi network (TGN)38, and β-COP and is distinct from the endoplasmic reticulum markers calnexin and Bip. Liver Golgi membranes and other vesicular compartment markers cosediment in vitro with βIII spectrin. βIII spectrin thus constitutes a major component of the Golgi and vesicular membrane skeletons.

Effects of elevated atmospheric CO2 concentration on leaf dark respiration of Xanthium strumarium in light and in darkness

Leaf dark respiration (R) is an important component of plant carbon balance, but the effects of rising atmospheric CO2 on leaf R during illumination are largely unknown. We studied the effects of elevated CO2 on leaf R in light (RL) and in darkness (RD) in Xanthium strumarium at different developmental stages. Leaf RL was estimated by using the Kok method, whereas leaf RD was measured as the rate of CO2 efflux at zero light. Leaf RL and RD were significantly higher at elevated than at ambient CO2 throughout the growing period. Elevated CO2 increased the ratio of leaf RL to net photosynthesis at saturated light (Amax) when plants were young and also after flowering, but the ratio of leaf RD to Amax was unaffected by CO2 levels. Leaf RN was significantly higher at the beginning but significantly lower at the end of the growing period in elevated CO2-grown plants. The ratio of leaf RL to RD was used to estimate the effect of light on leaf R during the day. We found that light inhibited leaf R at both CO2 concentrations but to a lesser degree for elevated (17–24%) than for ambient (29–35%) CO2-grown plants, presumably because elevated CO2-grown plants had a higher demand for energy and carbon skeletons than ambient CO2-grown plants in light. Our results suggest that using the CO2 efflux rate, determined by shading leaves during the day, as a measure for leaf R is likely to underestimate carbon loss from elevated CO2-grown plants.

Purification and Characterization of NADP+-Linked Isocitrate Dehydrogenase from Scots Pine1 : Evidence for Different Physiological Roles of the Enzyme in Primary Development

NADP+-isocitrate dehydrogenase (NADP+-IDH; EC 1.1.1.42) is involved in the supply of 2-oxoglutarate for ammonia assimilation and glutamate synthesis in higher plants through the glutamine synthetase/glutamate synthase (GS/GOGAT) cycle. Only one NADP+-IDH form of cytosolic localization was detected in green cotyledons of pine (Pinus spp.) seedlings. The pine enzyme was purified and exhibited molecular and kinetic properties similar to those described for NADP+-IDH from angiosperm, with a higher catalytic efficiency (105 m−1 s−1) than the deduced efficiencies for GS and GOGAT in higher plants. A polyclonal antiserum was raised against pine NADP+-IDH and used to assess protein expression in the seedlings. Steady-state levels of NADP+-IDH were coordinated with GS during seed germination and were associated with GS/GOGAT enzymes during chloroplast biogenesis, suggesting that NADP+-IDH is involved in the provision of carbon skeletons for the synthesis of nitrogen-containing molecules. However, a noncoordinated pattern of NADP+-IDH and GS/GOGAT was observed in advanced stages of cotyledon development and in the hypocotyl. A detailed analysis in hypocotyl sections revealed that NADP+-IDH abundance was inversely correlated with the presence of GS, GOGAT, and ribulose-1,5-bisphosphate carboxylase/oxygenase but was associated with the differentiation of the organ. These results cannot be explained by the accepted role of the enzyme in nitrogen assimilation and strongly suggest that NADP+-IDH may have other, as-yet-unknown, biological functions.

Skeletal matrices, muci, and the origin of invertebrate calcification.

The sudden appearance of calcified skeletons among many different invertebrate taxa at the Precambrian-Cambrian transition may have required minor reorganization of preexisting secretory functions. In particular, features of the skeletal organic matrix responsible for regulating crystal growth by inhibition may be derived from mucous epithelial excretions. The latter would have prevented spontaneous calcium carbonate overcrusting of soft tissues exposed to the highly supersaturated Late Proterozoic ocean [Knoll, A. H., Fairchild, I. J. & Swett, K. (1993) Palaios 8, 512-525], a putative function for which we propose the term "anticalcification." We tested this hypothesis by comparing the serological properties of skeletal water-soluble matrices and mucous excretions of three invertebrates--the scleractinian coral Galaxea fascicularis and the bivalve molluscs Mytilus edulis and Mercenaria mercenaria. Crossreactivities recorded between muci and skeletal water-soluble matrices suggest that these different secretory products have a high degree of homology. Furthermore, freshly extracted muci of Mytilus were found to inhibit calcium carbonate precipitation in solution.