Performance data of the coral Pocillopora verrucosa and environmental conditions along the Saudi Arabian Red Sea coast as assessed during 3 expeditions in the years 2011 and 2012

Large scale patterns of ecologically relevant traits may help identify drivers of their variability and conditions beneficial or adverse to the expression of these traits. Antimicrofouling defenses in scleractinian corals regulate the establishment of the associated biofilm as well as the risks of infection. The Saudi Arabian Red Sea coast features a pronounced thermal and nutritional gradient including regions and seasons with potentially stressful conditions to corals. Assessing the patterns of antimicrofouling defenses across the Red Sea may hint at the susceptibility of corals to global change. We investigated microfouling pressure as well as the relative strength of 2 alternative antimicrofouling defenses (chemical antisettlement activity, mucus release) along the pronounced environmental gradient along the Saudi Arabian Red Sea coast in 2 successive years. Microfouling pressure was exceptionally low along most of the coast but sharply increased at the southernmost sites. Mucus release correlated with temperature. Chemical defense tended to anti-correlate with mucus release. As a result, the combined action of mucus release and chemical antimicrofouling defense seemed to warrant sufficient defense against microbes along the entire coast. In the future, however, we expect enhanced energetic strain on corals when warming and/or eutrophication lead to higher bacterial fouling pressure and a shift towards putatively more costly defense by mucus release.

Lacunarity of the Spatial Distributions of Soil Types in Europe.

Lacunarity as a means of quantifying textural properties of spatial distributions suggests a classification into three main classes of the most abundant soils that cover 92% of Europe. Soils with a well-defined self-similar structure of the linear class are related to widespread spatial patterns that are nondominant but ubiquitous at continental scale. Fractal techniques have been increasingly and successfully applied to identify and describe spatial patterns in natural sciences. However, objects with the same fractal dimension can show very different optical properties because of their spatial arrangement. This work focuses primary attention on the geometrical structure of the geographical patterns of soils in Europe. We made use of the European Soil Database to estimate lacunarity indexes of the most abundant soils that cover 92% of the surface of Europe and investigated textural properties of their spatial distribution. We observed three main classes corresponding to three different patterns that displayed the graphs of lacunarity functions, that is, linear, convex, and mixed. They correspond respectively to homogeneous or self-similar, heterogeneous or clustered and those in which behavior can change at different ranges of scales. Finally, we discuss the pedological implications of that classification.

Effect of strain and magnetic field on the critical current and electric resistance of the joints between HTS coated conductors

Engineering of devices and systems such as magnets, fault current limiters or cables, based on High Temperature Superconducting wires requires a deep characterization of the possible degradation of their properties by handling at room temperature as well as during the service life thus establishing the limits for building up functional devices and systems. In the present work we report our study regarding the mechanical behavior of spliced joints between commercial HTS coated conductors based on YBCO at room temperature and service temperature, 77 K. Tensile tests under axial stress and the evolution of the critical current and the electric resistance of the joints have been measured. The complete strain contour for the tape and the joint has been obtained by using Digital Image Correlation. Also, tensile tests under external magnetic field have been performed and the effect of the applied field on the critical current and the electric resistance of the joints has been studied. Finally, a preliminary numerical study by means of Finite Element Method (FEM) of the mechanical behavior of the joints between commercial HTS is presented.

Effects of the water level on the flow topology over the Bolund island

We have analyzed the influence of the actual height of Bolund island above water level on different full-scale statistics of the velocity field over the peninsula. Our analysis is focused on the database of 10-minute statistics provided by Risø-DTU for the Bolund Blind Experiment. We have considered 10-minut.e periods with near-neutral atmospheric conditions, mean wind speed values in the interval [5,20] m/s, and westerly wind directions. As expected, statistics such as speed-up, normalized increase of turbulent kinetic energy and probability of recirculating flow show a large dependence on the emerged height of the island for the locations close to the escarpment. For the published ensemble mean values of speed-up and normalized increase of turbulent kinetic energy in these locations, we propose that some ammount of uncertainty could be explained as a deterministic dependence of the flow field statistics upon the actual height of the Bolund island above the sea level

Effects of the water level on the flow topology over the Bolund island.

We have analyzed the influence of the actual height of Bolund island above water level on different full-scale statistics of the velocity field over the peninsula. Our analysis is focused on the database of 10-minute statistics provided by Risø-DTU for the Bolund Blind Experiment. We have considered 10-minut.e periods with near-neutral atmospheric conditions, mean wind speed values in the interval [5,20] m/s, and westerly wind directions. As expected, statistics such as speed-up, normalized increase of turbulent kinetic energy and probability of recirculating flow show a large dependence on the emerged height of the island for the locations close to the escarpment. For the published ensemble mean values of speed-up and normalized increase of turbulent kinetic energy in these locations, we propose that some ammount of uncertainty could be explained as a deterministic dependence of the flow field statistics upon the actual height of the Bolund island above the sea level.

The underlying pathway structure of biochemical reaction networks

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function.

Structure and function of the Bacillus hybrid enzyme GluXyn-1: Native-like jellyroll fold preserved after insertion of autonomous globular domain

The 1,3–1,4-β-glucanase from Bacillus macerans (wtGLU) and the 1,4-β-xylanase from Bacillus subtilis (wtXYN) are both single-domain jellyroll proteins catalyzing similar enzymatic reactions. In the fusion protein GluXyn-1, the two proteins are joined by insertion of the entire XYN domain into a surface loop of cpMAC-57, a circularly permuted variant of wtGLU. GluXyn-1 was generated by protein engineering methods, produced in Escherichia coli and shown to fold spontaneously and have both enzymatic activities at wild-type level. The crystal structure of GluXyn-1 was determined at 2.1 Å resolution and refined to R = 17.7% and R(free) = 22.4%. It shows nearly ideal, native-like folding of both protein domains and a small, but significant hinge bending between the domains. The active sites are independent and accessible explaining the observed enzymatic activity. Because in GluXyn-1 the complete XYN domain is inserted into the compact folding unit of GLU, the wild-type-like activity and tertiary structure of the latter proves that the folding process of GLU does not depend on intramolecular interactions that are short-ranged in the sequence. Insertion fusions of the GluXyn-1 type may prove to be an easy route toward more stable bifunctional proteins in which the two parts are more closely associated than in linear end-to-end protein fusions.

Peropsin, a novel visual pigment-like protein located in the apical microvilli of the retinal pigment epithelium

A visual pigment-like protein, referred to as peropsin, has been identified by large-scale sequencing of cDNAs derived from human ocular tissues. The corresponding mRNA was found only in the eye, where it is localized to the retinal pigment epithelium (RPE). Peropsin immunoreactivity, visualized by light and electron microscopy, localizes the protein to the apical face of the RPE, and most prominently to the microvilli that surround the photoreceptor outer segments. These observations suggest that peropsin may play a role in RPE physiology either by detecting light directly or by monitoring the concentration of retinoids or other photoreceptor-derived compounds.

Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose

The SQD1 enzyme is believed to be involved in the biosynthesis of the sulfoquinovosyl headgroup of plant sulfolipids, catalyzing the transfer of SO3− to UDP-glucose. We have determined the structure of the complex of SQD1 from Arabidopsis thaliana with NAD+ and the putative substrate UDP-glucose at 1.6-Å resolution. Both bound ligands are completely buried within the binding cleft, along with an internal solvent cavity which is the likely binding site for the, as yet, unidentified sulfur-donor substrate. SQD1 is a member of the short-chain dehydrogenase/reductase (SDR) family of enzymes, and its structure shows a conservation of the SDR catalytic residues. Among several highly conserved catalytic residues, Thr-145 forms unusually short hydrogen bonds with both susceptible hydroxyls of UDP-glucose. A His side chain may also be catalytically important in the sulfonation.

NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans

The solution structure of the three-heme electron transfer protein cytochrome c7 from Desulfuromonas acetoxidans is reported. The determination of the structure is obtained through NMR spectroscopy on the fully oxidized, paramagnetic form. The richness of structural motifs and the presence of three prosthetic groups in a protein of 68 residues is discussed in comparison with the four-heme cytochromes c3 already characterized through x-ray crystallography. In particular, the orientation of the three hemes present in cytochrome c7 is similar to that of three out of four hemes of cytochromes c3. The reduction potentials of the individual hemes, which have been obtained through the sequence-specific assignment of the heme resonances, are discussed with respect to the properties of the protein matrix. This information is relevant for any attempt to understand the electron transfer pathway.

The crystal structure of modified bovine fibrinogen

Here we report the crystal structure at ≈4-Å resolution of a selectively proteolyzed bovine fibrinogen. This key component in hemostasis is an elongated 340-kDa glycoprotein in the plasma that upon activation by thrombin self-assembles to form the fibrin clot. The crystals are unusual because they are made up of end-to-end bonded molecules that form flexible filaments. We have visualized the entire coiled-coil region of the molecule, which has a planar sigmoidal shape. The primary polymerization receptor pockets at the ends of the molecule face the same way throughout the end-to-end bonded filaments, and based on this conformation, we have developed an improved model of the two-stranded protofibril that is the basic building block in fibrin. Near the middle of the coiled-coil region, the plasmin-sensitive segment is a hinge about which the molecule adopts different conformations. This segment also includes the boundary between the three- and four-stranded portions of the coiled coil, indicating the location on the backbone that anchors the extended flexible Aα arm. We suggest that a flexible branch point in the molecule may help accommodate variability in the structure of the fibrin clot.

Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products

The structures of complex polyketide natural products, such as erythromycin, are programmed by multifunctional polyketide synthases (PKSs) that contain modular arrangements of functional domains. The colinearity between the activities of modular PKS domains and structure of the polyketide product portends the generation of novel organic compounds—“unnatural” natural products—by genetic manipulation. We have engineered the erythromycin polyketide synthase genes to effect combinatorial alterations of catalytic activities in the biosynthetic pathway, generating a library of >50 macrolides that would be impractical to produce by chemical methods. The library includes examples of analogs with one, two, and three altered carbon centers of the polyketide products. The manipulation of multiple biosynthetic steps in a PKS is an important milestone toward the goal of producing large libraries of unnatural natural products for biological and pharmaceutical applications.