Cryptic invertebrates on subtidal rocky reefs vary with microhabitat structure and protection from fishing

The deployment of flat concrete blocks on subtidal rocky reefs can replicate natural reef microhabitats and provides a means for standardized sampling of cryptic invertebrates. The shape of the cavity beneath the block is related to reef topography and may influence the invertebrate community by affecting the amount of space for cryptic fauna to colonise and influencing the effectiveness of their predator-defence mechanisms. To determine the effect of sub-block reef structure and different levels of external predators on cryptic molluscs and echinoderms, I deployed concrete blocks at locations inside and outside the Maria Island marine reserve in eastern Tasmania, Australia. Relationships between sub-block reef structure and the cryptic invertebrate assemblage were evident between locations, whereas only a small but significant proportion of variation of assemblages between blocks within location was explained by reef surface area. No clear association with external predation pressure was evident in multivariate analyses of variation in assemblage structure. Juvenile abalone Haliotis rubra were not influenced by micro-habitat structure but were significantly less abundant at protected locations, the only species to exhibit such a response. This result follows a decline of emergent adult abalone in the marine reserve and raises the possibility of recruitment failure of abalone at some fully protected locations in the longer term.

In-situ X-ray micro-diffraction studies of heterogeneous interfaces between cementitious materials and geological formations

In the present study the challenge of analyzing complex micro X-ray diffraction (microXRD) patterns from cement–clay interfaces has been addressed. In order to extract the maximum information concerning both the spatial distribution and the crystal structure type associated with each of the many diffracting grains in heterogeneous, polycrystalline samples, an approach has been developed in which microXRD was applied to thin sections which were rotated in the X-ray beam. The data analysis, performed on microXRD patterns collected from a filled vein of a cement–clay interface from the natural analogue in Maqarin (Jordan), and a sample from a two-year-old altered interface between cement and argillaceous rock, demonstrate the potential of this method.

3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.

Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.

Nanometer-size anisotropy of injection-molded polymer micro-cantilever arrays

Understanding and controlling the structural anisotropies of injection-molded polymers is vital for designing products such as cantilever-based sensors. Such micro-cantilevers are considered as cost-effective alternatives to single-crystalline silicon-based sensors. In order to achieve similar sensing characteristics,structure and morphology have to be controlled by means of processing parameters including mold temperature and injection speed. Synchrotron radiation-based scanning small- (SAXS) and wide-angle x-ray scattering techniques were used to quantify crystallinity and anisotropy in polymer micro-cantilevers with micrometer resolution in real space. SAXS measurements confirmed the lamellar nature of the injection-molded semi-crystalline micro-cantilevers. The homogenous cantilever material exhibits a lamellar periodicity increasing with mold temperature but not with injection speed. We demonstrate that micro-cantilevers made of semi-crystalline polymers such as polyvinylidenefluoride, polyoxymethylene, and polypropylene show the expected strong degree of anisotropy along the injection direction.

Developmental Changes in the Structure and Composition of the Postsynaptic Density

The development of the brain and its underlying circuitry is dependent on the formation of trillions of chemical synapses, which are highly specialized contacts that regulate the flow of information from one neuron to the next. It is through these synaptic connections that neurons wire together into networks capable of performing specific tasks, and activity-dependent changes in their structural and physiological state is one way that the brain is thought to adapt and store information. At the ultrastructural level, developmental and activity-dependent changes in the size and shape of dendritic spines have been well documented, and it is widely believed that structural changes in spines are a hallmark sign of synapse maturation and alteration of synaptic physiology. While changes in spine structure have been studied extensively, changes in one of its most prominent components, the postsynaptic density (PSD), have largely evaded observation. The PSD is a protein-rich organelle on the cytoplasmic side of the postsynaptic membrane, where it sits in direct opposition to the presynaptic terminal. The PSD functions both to cluster neurotransmitter receptors at the cell surface as well as organize the intracellular signaling molecules responsible for transducing extracellular signals to the postsynaptic cell. Much is known about the chemical composition of the PSD, but the structural arrangement of its molecular components is not well documented. Adding to the difficulty of understanding such a complex mass of protein machinery is the fact that its protein composition is known to change in response to synaptic activity, meaning that its structure is plastic and no two PSDs are identical. Here, immuno-gold labeling and electron tomography of PSDs isolated throughout development was used to track changes in both the structure and molecular composition of the PSD. State-of-the-art cryo-electron tomography was used to study the fine structure of the PSD during development, and provides an unprecedented glimpse into its molecular architecture in an un-fixed, unstained and hydrated state. Through this analysis, large structural and compositional changes are apparent and suggest a model by which the PSD is first assembled as a mesh-like lattice of proteins that function as support for the later recruitment of various PSD components. Spatial analysis of the recruitment of proteins into the PSD demonstrated that its assembly has an underlying order.

An in situ surface electrochemistry approach towards whole-cell studies: the structure and reactivity of a Geobacter sulfurreducens submonolayer on electrified metal/electrolyte interfaces

A direct electron transfer process between bacterial cells of electrogenic species Geobacter sulfurreducens (Gs) and electrified electrode surfaces was studied to exploit the reactivity of Gs submonolayers on gold and silver surfaces. A submonolayer of Gs was prepared and studied to explore specifically the heterogeneous electron transfer properties at the bacteria/electrode interface. In situ microscopic techniques characterised the morphology of the Gs submonolayers under the operating conditions. In addition, complementary in situ spectroscopic techniques that allowed us to access in situ molecular information of the Gs with high surface selectivity and sensitivity were employed. The results provided clear evidence that the outermost cytochrome C in Gs is responsible for the heterogeneous electron transfer, which is in direct contact with the metal electrode. Feasibility of single cell in situ studies under operating conditions was demonstrated where the combination of surface-electrochemical tools at the nano- and micro-scale with microbiological approaches can offer unique opportunities for the emerging field of electro-microbiology to explore processes and interactions between microorganisms and electrical devices.

Animations of micro-computed tomography of a pleistocene terebratulid brachiopod

The dorsal valve of a Pleistocene terebratulid brachiopod, Terebratula scillae Seguenza, 1871, has developed a malignant cyst due to colonization in vivo by an endolithic sponge.This trace fossil is a compound boring and bioclaustration structure, representing a boring that has grown in unison with the growth of the cyst. The brachiopod has grown to adult size and growthlines indicate that it was colonised by the sponge when about half grown. Malformation of the shell may not have caused the death of the brachiopod and the sponge does not appear to have outlived its host; both symbionts seem to have died more or less simultaneously. This minus-minus relationship of two symbionts is considered to be a case of 'accidental symbiosis'.

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

Community Structure in Soil Porous System

Diffusion controls the gaseous transport process in soils when advective transport is almost null. Knowledge of the soil structure and pore connectivity are critical issues to understand and modelling soil aeration, sequestration or emission of greenhouse gasses, volatilization of volatile organic chemicals among other phenomena. In the last decades these issues increased our attention as scientist have realize that soil is one of the most complex materials on the earth, within which many biological, physical and chemical processes that support life and affect climate change take place. A quantitative and explicit characterization of soil structure is difficult because of the complexity of the pore space. This is the main reason why most theoretical approaches to soil porosity are idealizations to simplify this system. In this work, we proposed a more realistic attempt to capture the complexity of the system developing a model that considers the size and location of pores in order to relate them into a network. In the model we interpret porous soils as heterogeneous networks where pores are represented by nodes, characterized by their size and spatial location, and the links representing flows between them. In this work we perform an analysis of the community structure of porous media of soils represented as networks. For different real soils samples, modelled as heterogeneous complex networks, spatial communities of pores have been detected depending on the values of the parameters of the porous soil model used. These types of models are named as Heterogeneous Preferential Attachment (HPA). Developing an exhaustive analysis of the model, analytical solutions are obtained for the degree densities and degree distribution of the pore networks generated by the model in the thermodynamic limit and shown that the networks exhibit similar properties to those observed in other complex networks. With the aim to study in more detail topological properties of these networks, the presence of soil pore community structures is studied. The detection of communities of pores, as groups densely connected with only sparser connections between groups, could contribute to understand the mechanisms of the diffusion phenomena in soils.

Micro-scale habitat associations of woody plants in a neotropical cloud forest

Species?habitat associations may contribute to the maintenance of species richness in tropical forests, but previous research has been conducted almost exclusively in lowland forests and has emphasized the importance of topography and edaphic conditions. Is the distribution of woody plant species in a Peruvian cloud forest determined by microhabitat conditions? What is the role of environmental characteristics and forest structure in habitat partitioning in a tropical cloud forest? We examined species?habitat associations in three 1-ha plots using the torus-translation method. We used three different criteria to define habitats for habitat partitioning analyses, based on microtopography, forest structure and both sets of factors. The number of species associated either positively or negatively with each habitat was assessed. Habitats defined on the basis of environmental conditions and forest structure discriminated a greater number of positive and negative associations at the scale of our analyses in a tropical cloud forest. Both topographic conditions and forest structure contribute to small-scale microhabitat partitioning of woody plant species in a Peruvian tropical cloud forest. Nevertheless, canopy species were most correlated with the distribution of environmental variables, while understorey species displayed associations with forest structure.

Analysis of Meshfree Methods for Lagrangian Fluid-Structure Interaction

In this dissertation a new numerical method for solving Fluid-Structure Interaction (FSI) problems in a Lagrangian framework is developed, where solids of different constitutive laws can suffer very large deformations and fluids are considered to be newtonian and incompressible. For that, we first introduce a meshless discretization based on local maximum-entropy interpolants. This allows to discretize a spatial domain with no need of tessellation, avoiding the mesh limitations. Later, the Stokes flow problem is studied. The Galerkin meshless method based on a max-ent scheme for this problem suffers from instabilities, and therefore stabilization techniques are discussed and analyzed. An unconditionally stable method is finally formulated based on a Douglas-Wang stabilization. Then, a Langrangian expression for fluid mechanics is derived. This allows us to establish a common framework for fluid and solid domains, such that interaction can be naturally accounted. The resulting equations are also in the need of stabilization, what is corrected with an analogous technique as for the Stokes problem. The fully Lagrangian framework for fluid/solid interaction is completed with simple point-to-point and point-to-surface contact algorithms. The method is finally validated, and some numerical examples show the potential scope of applications.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Effects of nutrition on digestión efficiency and gaseous emissions from slurry in growing pigs: III. Influence of varying the dietary level of calcium soap of palm fatty acids distillate with or without orange pulp supplemention

The aim of this study was to establish the relationships between faecal fat concentration and gaseous emissions from pig slurry. Five diets were designed to meet essential nutrient requirements: a control and four experimental feeds including two levels (35 or 70 g/kg) of calcium soap fatty acids distillate (CSP) and 0 or 200 g/kg of orange pulp (OP) combined in a 2 × 2 factorial structure. Thirty growing pigs (six per treatment) were used to measure dry matter (DM) and N balance, coefficients of total tract apparent digestibility (CTTAD) of nutrients, faecal and urine composition and potential emissions of ammonia (NH3) and methane (CH4). Increasing dietary CSP level decreased DM, ether extract (EE) and crude protein (CP) CTTAD (by 4.0, 11.1 and 3.5%, respectively, P < 0.05), but did not influence those of fibrous constituents. It also led to a decrease (from 475 to 412 g/kg DM, P < 0.001) of faecal concentration of neutral detergent fibre (aNDFom) and to an increment (from 138 to 204 g/kg, P < 0.001) of EE in faecal DM that was related to greater CH4 emissions, both per gram of organic matter (P = 0.021) or on a daily basis (P < 0.001). Level of CSP did not affect N content in faeces or urine, but increased daily DM (P < 0.001), and N (P = 0.031) faecal excretion with no effect on urine N excretion. This resulted in lesser (P = 0.036) NH3 potential emission per kg of slurry. Addition of OP decreased CTTAD of EE (by 7.9%, P = 0.044), but increased (P < 0.05) that of all the fibrous fractions. As a consequence, faecal EE content increased (from 165 to 177 g/kg DM; P = 0.012), and aNDFom decreased greatly (from 483 to 404 g/kg DM, P < 0.001), which in all resulted in a lack of effect of OP on CH4 potential emission. Inclusion of OP in the diet also led to a significant decrease of CP CTTAD (by 6.85%, P < 0.001), and to an increase of faecal CP concentration (from 174 to 226 g/kg DM, P < 0.001), with no significant influence on urine N content. These effects resulted in higher N faecal losses, especially those of the undigested dietary origin, without significant effects on potential NH3 emission. No significant interactions between CSP and OP supplementation were observed for the gaseous emissions measured.

ASSOCIATIVISMO EMPRESARIAL ENTRE MICRO E PEQUENAS EMPRESAS: A EXPERIÊNCIA DO GRANDE ABC COM O PROJETO EMPREENDER (SEBRAE)

O associativismo empresarial aparece como forma de desenvolvimento regional, seja este econômico, social ou cultural, e é grande aliado para o surgimento e crescimento das micro e pequenas empresas. É um tema já vivenciado e estudado por vários países do mundo, entre eles europeus e especificamente italianos, mas ainda pouco estudado e conhecido no Brasil. A presente pesquisa objetivou analisar o associativismo empresarial entre micro e pequenas empresas (MPEs) na região do Grande ABC (GABC) pelo Projeto Empreender (SEBRAE) relacionando seus dados com os publicados do relatório 2003/5 de autoria do Observatório Europeu de estudos sobre pequenas e médias empresas europeias, analisando as formas de associativismo aqui ocorridas, além de identificar o perfil das empresas e empresários envolvidos no projeto. Para tal análise foram coletados dados de um total de 63 empresas do Projeto Empreender, nos núcleos de Santo André, São Caetano do Sul e Ribeirão Pires. Do GABC foram coletados dados utilizando o instrumento desenvolvido pelo Observatório Europeu de estudos sobre pequenas e médias empresas. A análise dos dados coletados no GABC em relação aos dados europeus se fez necessária para que pudessem ser encontrados pontos de divergências e convergências em cada uma das experiências, objetivando o aprendizado e evolução do tema. A escolha do GABC foi motivada pelo fato da região passar por mudanças no seu perfil econômico, passando de berço e grande pólo das grandes indústrias para um grande centro de pequenas empresas prestadoras de serviços. Após coleta e análise dos dados, percebeu-se que a experiência do GABC e a ocorrida na Itália se parecem em muitos aspectos, porém tem grandes diferenças estruturais. Enquanto o projeto europeu é de responsabilidade de um órgão da União Europeia, aqui o projeto é de autoria do SEBRAE e sofre grandes conflitos com as Associações Comerciais e Industriais (ACIs) da região quando o tema é custeio das despesas das pessoas e estrutura que envolve a implantação do projeto. Além disso, conclui-se que é necessária uma maior aproximação dos municípios com o projeto, tendo em vista que isto poderia ser fator de incentivo a entrada de novas empresas além de fator de aumento de seriedade do sistema. Mais dois dados merecem destaque. Primeiro o fato do Projeto Empreender ter pouca visibilidade regional, ou seja, ser muito pouco divulgado, e o fato da agência de desenvolvimento do GABC não ter aproximação alguma com o projeto. Por último, surgem dados no decorrer da pesquisa que rompem a barreira das teorias administrativas conhecidas, tais como a amizade como fator de associativismo. Portanto, os resultados obtidos com essa pesquisa apontam para a influência no incentivo ao desenvolvimento do processo associativista na região do GABC, além de servir como incentivador para a aproximação de outros atores sociais no processo.(AU)