GPI-specific phospholipase D (GPI-PLD) is expressed during mouse development and is localized to the extracellular matrix of the developing mouse skeleton

Glycosylphosphatidylinositol-specific phospholipase D (GPI-PLD) is abundant in serum and has a well-characterized biochemistry; however, its physiological role is completely unknown. Previous investigations into GPI-PLD have focused on the adult animal or on in vitro systems and a putative role in development has been neither proposed nor investigated. We describe the first evidence of GPI-PLD expression during mouse embryonic ossification. GPI-PLD expression was detected predominantly at sites of skeletal development, increasing during the course of gestation. GPI-PLD was observed during both intramembraneous and endochondral ossification and localized predominantly to the extracellular matrix of chondrocytes and to primary trabeculae of the skeleton. In addition, the mouse chondrocyte cell line ATDC5 expressed GPI-PLD after experimental induction of differentiation. These results implicate GPI-PLD in the process of bone formation during mouse embryogenesis.

The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

Background: Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective: To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods: The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results: To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions: The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms.

{\it Hox\/} genes and specification of regional identity in the axial skeleton: Analysis of the individual and combined mutant phenotypes of the paralogous group 4 murine {\it Hox\/} genes; {\it hoxa\/}-4, {\it hoxb\/}-4 and {\it hoxd\/}-4

The Hox gene products are transcription factors involved in specifying regional identity along the anteroposterior body axis. In Drosophila, where these genes are known as HOM-C (Homeotic-complex) genes and where they have been most extensively studied, they are expressed in restricted domains along the anteroposterior axis with different anterior limits. Genetic analysis of a large number of gain- and loss-of-function alleles of these genes has revealed that these genes are important in specifying segmental identity at their anterior limits of expression. Furthermore, there is a functional dominance of posterior genes over anterior genes, such that posterior genes can dominantly specify their developmental programs in spite of the expression of more anterior genes in the same segment. In the mouse, there are four clusters of HOM-C genes, called Hox genes. Thus, there may be up to four genes, called paralogs, that are more highly homologous to each other and to their Drosophila homolog than they are to the other mouse Hox genes. The single mutants for two paralogous genes, hoxa-4 and hoxd-4, presented in this dissertation, are similar to several other mouse Hox mutants in that they show partial, incompletely penetrant homeotic transformations of vertebrae at their anterior limit of expression. These mutants were then bred with hoxb-4 mutants (Ramirez-Solis, et al. 1993) to generate the three possible double mutant combinations as well as the triple mutant. The skeletal phenotypes of these group 4 Hox compound mutants displayed clear alterations in regional identity, such that a nearly complete transformation towards the morphology of the first cervical vertebra occurs. These results suggest a certain degree of functional redundancy among paralogous genes in specifying regional identity. Furthermore, there was a remarkable dose-dependent increase in the number of vertebrae transformed to a first cervical vertebra identity, including the second through the fifth cervical vertebrae in the triple mutant. Thus, these genes are required in a larger anteroposterior domain than is revealed by the single mutant phenotypes alone, such that multiple mutations in these genes result in transformations of vertebrae that are not at their anterior limit of expression. ^

Granular computing as a tool of human data interaction - a cognitive cities use case

The article proposes granular computing as a theoretical, formal and methodological basis for the newly emerging research field of human–data interaction (HDI). We argue that the ability to represent and reason with information granules is a prerequisite for data legibility. As such, it allows for extending the research agenda of HDI to encompass the topic of collective intelligence amplification, which is seen as an opportunity of today’s increasingly pervasive computing environments. As an example of collective intelligence amplification in HDI, we introduce a collaborative urban planning use case in a cognitive city environment and show how an iterative process of user input and human-oriented automated data processing can support collective decision making. As a basis for automated human-oriented data processing, we use the spatial granular calculus of granular geometry.

Granular flow in polymineralic rocks bearing sheet silicates: New evidence from natural examples

Natural deformation in carbonate mylonites bearing sheet silicates occurs via a complex interaction of granular flow and solution transfer processes and involves continuous cycles of dissolution, grain boundary diffusion, nucleation and growth. In this way, new sheet silicates (a) nucleate within voids formed by grain boundary sliding of calcite grains. (b) grow, and (c) rotate towards the shear plane. As a consequence, small mica grains show a wide range of orientations with respect to the shear plane, but moderate to large grains are subparallel both to each other and to the shear plane. Increases of average grain sizes with increasing temperature of sheet silicates in mica-rich layers is more pronounced than in mica-poor layers. In the calcitic matrix however, sheet silicates can only grow via solution-precipitation and mass transfer processes. Therefore, the observed grain size variability indicates drastic differences in mass transfer behavior between the individual layers, which might be related to differences in the fluid flux. Based on these observations, a conceptual model for the microfabric evolution in sheet silicate bearing mylonites is presented. © 2001 Elsevier Science B.V. All rights reserved.

Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections.

High-resolution structural information on optimally preserved bacterial cells can be obtained with cryo-electron microscopy of vitreous sections. With the help of this technique, the existence of a periplasmic space between the plasma membrane and the thick peptidoglycan layer of the gram-positive bacteria Bacillus subtilis and Staphylococcus aureus was recently shown. This raises questions about the mode of polymerization of peptidoglycan. In the present study, we report the structure of the cell envelope of three gram-positive bacteria (B. subtilis, Streptococcus gordonii, and Enterococcus gallinarum). In the three cases, a previously undescribed granular layer adjacent to the plasma membrane is found in the periplasmic space. In order to better understand how nascent peptidoglycan is incorporated into the mature peptidoglycan, we investigated cellular regions known to represent the sites of cell wall production. Each of these sites possesses a specific structure. We propose a hypothetic model of peptidoglycan polymerization that accommodates these differences: peptidoglycan precursors could be exported from the cytoplasm to the periplasmic space, where they could diffuse until they would interact with the interface between the granular layer and the thick peptidoglycan layer. They could then polymerize with mature peptidoglycan. We report cytoplasmic structures at the E. gallinarum septum that could be interpreted as cytoskeletal elements driving cell division (FtsZ ring). Although immunoelectron microscopy and fluorescence microscopy studies have demonstrated the septal and cytoplasmic localization of FtsZ, direct visualization of in situ FtsZ filaments has not been obtained in any electron microscopy study of fixed and dehydrated bacteria.

Coordination of murine limb muscle, skeleton and connective tissue development by Lmx1b

The underlying genetic defects of a congenital disease Nail-Patella Syndrome are loss-of-function mutations in the LMX1B gene. Lmx1b encodes a LIM-homeodomain transcription factor that is expressed specifically in the dorsal limb bud mesenchyme. Gain- and loss-of-function experiments suggest that Lmx1b is both necessary and sufficient to specify dorsal limb patterning. However, how Lmx1b coordinates patterning of the dorsal tissues in the limb, including muscle, skeleton and connective tissues, remains unknown. One possibility is that each tissue specifies its own pattern cell-autonomously, i.e., Lmx1b is expressed in tissues in which it functions and different tissues do not communicate with each other. Another possibility is that tissues that express Lmx1b interact with adjacent tissues and provide patterning information thereby directing the development of tissues non-cell-autonomously. Previous results showed that Lmx1b is expressed in limb connective tissue and skeleton, but is not expressed in muscle tissue. Moreover, muscles and muscle connective tissue are closely associated during development. Therefore, we hypothesize that Lmx1b controls limb muscle dorsal-ventral (DV) patterning through muscle connective tissue, but regulates skeleton and tendon/ligament development cell-autonomously. ^ To test this hypothesis, we first examined when and where the limb dorsal-ventral asymmetry is established during development. Subsequently, conditional knockout and overexpression experiments were performed to delete or activate Lmx1b in different tissues within the limb. Our results show that deletion of Lmx1b from whole limb mesenchyme results in all dorsal tissues, including muscle, tendon/ligament and skeleton, transforming into ventral structures. Skeleton-specific knockout of Lmx1b led to the dorsal duplication of distal sesamoid and metacarpal bones, but did not affect the pattern formation of other tissues, suggesting that Lmx1b controls skeleton development cell-autonomously. In addition, this skeleton-specific pattern alteration only occurs in distal limb tissues, not proximal limb tissues, indicating different regulatory mechanisms operate along the limb proximal-distal axis. Moreover, skeleton-specific ectopic expression of Lmx1b reveals a complementary skeletal-specific dorsalized phenotype. This result supports a cell-autonomous role for Lmx1b in dorsal-ventral skeletal patterning. This study enriched our understanding of limb development, and the insights from this research may also be applicable for the development of other organs. ^

Abundances and ebridian skeleton contents from IODP Exp302

Abundant and diversified ebridians recovered during IODP Expedition 302 (ACEX) have been identified and counted in order to establish their taxonomy and to decipher the biostratigraphic potential of ebridians in the central Arctic Ocean. In the ACEX samples these fossils are preserved in Lithologic Units 1/6 and 2, which consist mainly of dark silty clay and biosiliceous ooze, respectively. Thirty taxa have been distinguished, three of which are described as new species (Ammmodochium lomonosovense, Pseudammodochium karyon, and pseudammodochium psichion). The most dominant ebridian species is Pseudammodochium dictyoides throughout the biosiliceous section. The second dominant species varies alternately throughout the section. Based on the characteristic occurrences of major ebridian taxa, the ebridian assemblageswere divided into GroupsAtoDin stratigraphic order. The ebridian assemblages in piston core USGS Fl-422 from the Alpha Ridge probably correlate to our assemblage Group A of early middle Eocene age, although rare younger taxa are irregularly included.

Morphological plasticity of the coral skeleton under CO2-driven seawater acidification

Ocean acidification causes corals to calcify at reduced rates, but current understanding of the underlying processes is limited. Here, we conduct a mechanistic study into how seawater acidification alters skeletal growth of the coral Stylophora pistillata. Reductions in colony calcification rates are manifested as increases in skeletal porosity at lower pH, while linear extension of skeletons remains unchanged. Inspection of the microstructure of skeletons and measurements of pH at the site of calcification indicate that dissolution is not responsible for changes in skeletal porosity. Instead, changes occur by enlargement of corallite-calyxes and thinning of associated skeletal elements, constituting a modification in skeleton architecture. We also detect increases in the organic matrix protein content of skeletons formed under lower pH. Overall, our study reveals that seawater acidification not only causes decreases in calcification, but can also cause morphological change of the coral skeleton to a more porous and potentially fragile phenotype.

Calcium isotope fractionation in cultured, modern and fossil scleractinian coral skeleton

The present study investigates the influence of environmental (temperature, salinity) and biological (growth rate, inter-generic variations) parameters on calcium isotope fractionation (d44/40Ca) in scleractinian coral skeleton to better constrain this record. Previous studies focused on the d44/40Ca record in different marine organisms to reconstruct seawater composition or temperature, but only few studies investigated corals. This study presents measurements performed on modern corals from natural environments (from the Maldives for modern and from Tahiti for fossil corals) as well as from laboratory cultures (Centre Scientifique de Monaco). Measurements on Porites sp., Acropora sp., Montipora verrucosa and Stylophora pistillata allow constraining inter-generic variability. Our results show that the fractionation of d44/40Ca ranges from 0.6 to 0.1 per mil, independent of the genus or the environmental conditions. No significant relationship between the rate of calcification and d44/40Ca was found. The weak temperature dependence reported in earlier studies is most probably not the only parameter that is responsible for the fractionation. Indeed, sub-seasonal temperature variations reconstructed by d18O and Sr/Ca ratio using a multi-proxy approach, are not mirrored in the coral's d44/40Ca variations. The intergeneric variability and intrageneric variability among the studied samples are weak except for S. pistillata, which shows calcium isotopic values increasing with salinity. The variability between samples cultured at a salinity of 40 is higher than those cultured at a salinity of 36 for this species. The present study reveals a strong biological control of the skeletal calcium isotope composition by the polyp and a weak influence of environmental factors, specifically temperature and salinity (except for S. pistillata). Vital effects have to be investigated in situ to better constrain their influence on the calcium isotopic signal. If vital effects could be extracted from the isotopic signal, the calcium isotopic composition of coral skeletons could provide reliable information on the calcium composition and budget in ocean.

Lagrangian skeleton on the Gulf of Mexico oil spill

The understanding of the circulation of ocean currents, the exchange of CO2 between atmosphere and oceans, and the influence of the oceans on the distribution of heat on a global scale is key to our ability to predict and assess the future evolution of climate [1, 2]. Global climate change is affecting sea breathing through mechanisms not yet understood.

On the generative equations of fractal self-similarity in granular media and the related PSD models

The physical appearance of granular media suggests the existence of geometrical scale invariance. The paper discuss how this physico-empirical property can be mathematically encoded leading to different generative models: a smooth one encoded by a differential equation and another encoded by an equation coming from a measure theoretical property.