Microbial boundstone dominated carbonate slope (Upper Carboniferous,N Spain): Microfacies,lithofacies distribution and stratal geometry

Summary The Carboniferous, particularly during the Serpukhovian and Bashkirian time, was a period of scarce shallow-water calcimicrobial-microbialite reef growth. Organic frameworks developed on high-rising platforms are, however, recorded in the Precaspian Basin subsurface, Kazakhstan, Russia, Japan and Spain and represent uncommon occurrences within the general trend of low accumulation rates and scarcity of shallow-water reefs. Sierra del Cuera (Cantabrian Mountains, N Spain) is a well-exposed high-rising carbonate platform of Late Carboniferous (Bashkirian-Moscovian) age with a microbial boundstone-dominated slope dipping from 20° up to 45°. Kilometer-scale continuous exposures allow the detailed documentation of slope geometry and lithofacies spatial distribution. This study aims to develop a depositional model of steep-margined Late Paleozoic platforms built by microbial carbonates and to contribute to the understanding of the controlling factors on lithofacies characteristics, stacking patterns, accumulation rates and evolution of the depositional architecture of systems, which differ from light-dependent coralgal platform margins. From the platform break to depths of nearly 300 m, the slope is dominated by massive cement-rich boundstone, which accumulated through the biologically induced precipitation of micrite. Boundstone facies (type A) with peloidal carbonate mud, fenestellid and fistuliporid bryozoans, sponge-like molds and primary cavities filled by radiaxial fibrous cement occurs all over the slope but dominates the deeper settings. Type B boundstone consists of globose centimeter-scale laminated accretionary structures, which commonly host botryoidal cement in growth cavities. The laminae nucleate around fenestellid bryozoans, sponges, Renalcis and Girvanella-like filaments. Type B boundstone typically occurs at depths between 20–150 m to locally more than 300 m and forms the bulk of the Bashkirian prograding slope. The uppermost slope boundstone (type C; between 0 and 20–100 m depth) includes peloidal micrite, radiaxial fibrous cement, bryozoans, sponge molds, Donezella, Renalcis, Girvanella, Ortonella, calcareous algae and calcitornellid foraminifers. From depths of 80–200 m to 450 m, 1–30 m thick lenses of crinoidal packstone, spiculitic wackestone, and bryozoan biocementstone with red-stained micrite matrix are episodically intercalated with boundstone and breccias. These layers increase in number from the uppermost Bashkirian to the Moscovian in parallel with the change from a rapidly prograding to an aggrading architecture. The red-stained strata share comparable features with Lower Carboniferous deeper-water mud-mound facies and were deposited during relative rises of sea level and pauses in boundstone production. Rapid relative sea-level rises might have been associated with changes in oceanographic conditions not favourable for thecalcimicrobial boundstone growth, such as upwelling of colder, nutrient-rich waters lifting the thermocline to depths of 80–200 m. Downslope of 150–300 m, boundstones interfinger with layers of matrix-free breccias, lenses of matrix-rich breccias, platform- and slope-derived grainstone and crinoidal packstone. Clast-supported breccias bound by radiaxial cement are produced by rock falls and avalanches coeval to boundstone growth. Matrix-rich breccias are debris flow deposits triggered by the accumulation of red-stained layers. Debris flows develop following the relative sea-level rises, which favour the deposition of micrite-rich lithofacies on the slope rather than being related to relative sea-level falls and subaerial exposures. The steep slope angles are the result of in situ growth and rapid stabilization by marine cement in the uppermost part, passing into a detrital talus, which rests at the angle of repose of noncohesive material. In the Moscovian, the aggradational architecture and steeper clinoforms are the result of increased accommodation space due to tectonic subsidence and due to a reduction of slope accumulation rates (from 240±45−605±35 m/My to 130±5 m/My). The increasing number of red-stained layers and the decrease of boundstone productivity are attributed to environmental changes in the adjacent basin, in particular during relative rises of sea level and to possible cooling due to icehouse conditions. The geometry of the depositional system appears to be controlled by boundstone growth rates. During the Bashkirian, the boundstone growth potential is at least 10 times greater than average values for ancient carbonate systems. The slope progradation rates (nearly 400–1000 m/My) are similar to the highest values deduced for the Holocene Bahamian prograding platform margin. The fundamental differences with modern systems are that progradation of the microbial-boundstone dominated steep slope is primarily controlled by boundstone growth rates rather than by highstand shedding from the platform top and that boundstone growth is largely independent from light and controlled by the physicochemical characteristics of seawater.     

Spherical Boundary Conditions: A Finite and System Size Independent Geometry for Simulations of Electrolytic Liquids

The system size dependence of the thermodynamic properties of electrolytic systems in "Spherical Boundary Conditions" (SBC) have been examined in this work. Coulombic systems were simulated with different system sizes (N ) for a wide range of concentrations, different ionic charges and solvent permittivities. The effects of system size upon the mean internal energy ?U? and mean ionic activity coefficient ?γ _±? values were determined. Our results indicated that there was no dependence of the thermodynamic properties upon system size in the non-Euclidean geometry. Different methods of extrapolating the thermodynamic properties to infinite numbers were studied in detail. In contrast to the Euclidean geometry, the method of extrapolating ?U? or ?γ _±? versus N ^-1, N ^-2/3 and N ^-1/3 was not statistically justifiable nor advantageous. Therefore, SBC is well suited to simulating systems involving long-range electrostatic interactions because the results do not dependent upon system size.     

Diastolic suction in heart failure: Impact of left ventricular geometry,untwist, and flow mechanics

Aims

Vector flow mapping (VFM) can be used to assess intraventricular hemodynamics quantitatively. This study assessed the magnitude of the suction flow kinetic energy with VFM and investigated the relation between left ventricular (LV) function and geometry in patients with an estimated elevated LV filling pressure.

Materials and methods

We studied 24 subjects with an elevated LV filling pressure (EFP group) and 36 normal subjects (normal group). Suction was defined as flow directed toward the apex during the period from soon after systolic ejection to before mitral inflow. The flow kinetic energy index was quantified as the sum of the product of the blood mass and velocity vector and its magnitude to the peak value was measured.

Key findings

Suction flow was observed in 12 (50%) EFP-group patients and 36 (100%) normal-group subjects. The magnitude of the suction kinetic energy index was significantly smaller in EFP versus normal group (2.7 ± 3.8 vs. 5.7 ± 4.4 g/s/cm², P < 0.01). The EFP-group patients with suction had a smaller LV end-systolic volume (ESV) (P < 0.01), greater ellipsoidal geometry (P < 0.05) and untwisting rate (P < 0.01) than the EFP-group patients without suction. A regression analysis indicated a significant linear relation between the suction kinetic energy index and LVEF (r = 0.43, P = 0.04), ESV (r = − 0.40, P = 0.05), eccentricity index (r = 0.44, P = 0.04), and untwisting rate (r = 0.51, P = 0.04).

Significance

The magnitude of the suction flow kinetic energy index derived from VFM may allow the quantitative assessment of the suction flow, which correlates with LV systolic function, geometry, and untwisting mechanics.     

Stratigraphy, geometry, and facies of a Middle Devonian ramp-to-basin transect (Eastern Anti-Atlas, SE Morocco)

Summary In the castern Anti-Atlas (SE Morocco), a small sedimentary basin (Mader Basin) evolved during the late Palacozoic. The Middle Devonian deposits consist of shales and limestones with a thickness up to 700 m in the depocentre. Sedimentary structures and sole marks of Middle Devonian limestones indicate transport from the northwest and the south towards the basin centre, located in the central Mader area. Lithostratigraphic, biostratigraphic, and dynamic stratigraphic approaches were applied to correlate stratigraphic sections. Five correlatable large-scale base-level hemicycles were recognized in the Middle Devonian succession. Thickness trends of Middle Devonian deposits, regional correlations, and facies-trends reveal the geometry of a carbonate ramp. The carbonate ramp was slightly inclined (<1°) to the NE. A sedimentary wedge, consisting of limestones and limestone/marl alternations, was deposited during the Eifelian and marks the transition from the ramp to the adjacent basin. Middle Devonian water depths are estimated as close to and within the storm wave-base at the southern area of the ramp and far below storm wave-base in the northeastern part of the ramp. Shallowest conditions (inner-ramp environment), close or within the fairweather wave-base, existed during the early Givetian as documented by the abundance of recfal fauna (stromatoporoids, corals) and calcimicrobes (lumps, micritic envelopes) in the eastern and southeastern area of the ramp.     

Catalytic cycle of human glutathione reductase near 1 A resolution

Efficient enzyme catalysis depends on exquisite details of structure beyond those resolvable in typical medium- and high-resolution crystallographic analyses. Here we report synchrotron-based cryocrystallographic studies of natural substrate complexes of the flavoenzyme human glutathione reductase (GR) at nominal resolutions between 1.1 and 0.95 Å that reveal new aspects of its mechanism. Compression in the active site causes overlapping van der Waals radii and distortion in the nicotinamide ring of the NADPH substrate, which enhances catalysis via stereoelectronic effects. The bound NADPH and redox-active disulfide are positioned optimally on opposite sides of the flavin for a 1,2-addition across a flavin double bond. The new structures extend earlier observations to reveal that the redox-active disulfide loop in GR is an extreme case of sequential peptide bonds systematically deviating from planarity—a net deviation of 53° across five residues. But this apparent strain is not a factor in catalysis, as it is present in both oxidized and reduced structures. Intriguingly, the flavin bond lengths in oxidized GR are intermediate between those expected for oxidized and reduced flavin, but we present evidence that this may not be due to the protein environment but instead due to partial synchrotron reduction of the flavin by the synchrotron beam. Finally, of more general relevance, we present evidence that the structures of synchrotron-reduced disulfide bonds cannot generally be used as reliable models for naturally reduced disulfide bonds.     

Allometric analysis of Sitka spruce branches: mechanical versus hydraulic design principles

The geometry of tree branches can have considerable effect on their efficiency in terms of carbon export per unit carbon investment in structure. The purpose of this study was to evaluate different design criteria using data describing the form of Picea sitchensis branches. Allometric analysis of the data suggests that resources are distributed to favour shoots with the greatest opportunity for extension into new space, with priority to the extension of the leader. The distribution of allometric relations of links (branch elements) was tested against two models: the pipe model, based on hydraulic transport requirements, and a static load model based on the requirement of shoots to provide mechanical resistance to static loads. Static load resistance required the load parameter to be proportional to the link radius raised to the power of 4. This was shown to be true within a 95% statistical confidence limit. The pipe model would require total distal length to be proportional to link radius squared but the measured branches did not conform well to this model. The comparison suggests that the diameters of branch elements were more related to the requirements for mechanical load. The cost of following a hydraulic design principle (the pipe model) in terms of mechanical efficiency was estimated and suggested that the pipe model branch would not be mechanically compromised but would use structural resources inefficiently. Resource allocation among branch elements was found to be consistent with mechanical stability criteria but also indicated the possibility of allocation based on other criteria, such as potential light interception by shoots. The evidence suggests that whilst branch topology increments by reiteration of units of morphogenesis, the geometry follows a functional design pattern.     

Role of conserved glycine in zinc-dependent medium chain dehydrogenase/reductase superfamily

The medium-chain dehydrogenase/reductase (MDR) superfamily consists of a large group of enzymes with a broad range of activities. Members of this superfamily are currently the subject of intensive investigation, but many aspects, including the zinc dependence of MDR superfamily proteins, have not yet have been adequately investigated. Using a density functional theory-based screening strategy, we have identified a strictly conserved glycine residue (Gly) in the zinc-dependent MDR superfamily. To elucidate the role of this conserved Gly in MDR, we carried out a comprehensive structural, functional, and computational analysis of four MDR enzymes through a series of studies including site-directed mutagenesis, isothermal titration calorimetry, electron paramagnetic resonance (EPR), quantum mechanics, and molecular mechanics analysis. Gly substitution by other amino acids posed a significant threat to the metal binding affinity and activity of MDR superfamily enzymes. Mutagenesis at the conserved Gly resulted in alterations in the coordination of the catalytic zinc ion, with concomitant changes in metal-ligand bond length, bond angle, and the affinity (K(d)) toward the zinc ion. The Gly mutants also showed different spectroscopic properties in EPR compared with those of the wild type, indicating that the binding geometries of the zinc to the zinc binding ligands were changed by the mutation. The present results demonstrate that the conserved Gly in the GHE motif plays a role in maintaining the metal binding affinity and the electronic state of the catalytic zinc ion during catalysis of the MDR superfamily enzymes.     

The structural and electrochemical consequences of hydrogenating copper N2S2 Schiff base macrocycles

A series of cis and trans tetradentate copper macrocyclic complexes, of ring size 14-16, that employ amine and thioether donor groups are reported. Apart from 5,6,15,16-bisbenzo-8,13-diaza-1,4-dithia-cyclohexadecane copper(I) (cis-[Cu(H₄N_buS_en)]⁺) all of the complexes are obtained in the copper(II) form. Crystallographic analysis shows that the copper(II) complexes all adopt a distorted planar geometry around the copper. In contrast, cis-[Cu(H₄N_buS_en)]⁺ is found to adopt a distorted tetrahedral geometry. The complexes were subjected to electrochemical analysis in water and acetonitrile. The effect of the solvent, positions of the donor atoms (cis/trans) on E^1/2 is discussed as is the comparison of the electrochemical behaviour of these complexes with their parent Schiff base macrocycles.     

Reorienting when cues conflict: A role for information content in spatial learning?

In two experiments, human participants searched in dynamic three-dimensional virtual-environment rectangular enclosures. Unlike previous studies involving learning of features and geometry, we trained features and geometry separately before placing them in conflict. Specifically, participants learned to respond to rewarded features located along the principle axis of a rectangular search space and to respond to rewarded geometry of a rectangular search space in separate training phases followed by a single test trial. During the test trial, features and geometry were placed in conflict by situating rewarded bins during feature training in unrewarded geometric corners from geometry training and unrewarded bins during feature training in rewarded geometric corners from geometry training. Results of Experiment 1 indicated that although all participants learned features and geometry at an equivalent rate and to an equivalent level, performance during the test trial indicated no preferential responding to features or geometry. However, choice reaction time was significantly longer during the test trial compared to that of last feature and last geometry training trials. Experiment 2 attempted to dissociate information content of features and geometry from their acquired associative strength by rewarding only one geometric corner during geometry training. Results of Experiment 2 indicated that although features had presumably acquired greater associative strength relative to that of geometry by the end of training, performance during the test trial indicated no preferential responding to features or geometry. As in Experiment 1, choice reaction time was significantly longer during the test trial compared to that of last feature and last geometry training trials. Collectively, results seem to provide converging evidence against a view-based matching account of spatial learning, appear inconsistent with standard associative-based accounts of spatial learning, and suggest that information content of spatial cues may play an important role in spatial learning.     

Modeling the effects of enclosure size on geometry learning

Several recent studies have shown that chickens, fish, and humans trained to find a reward in a corner of a rectangular enclosure with distinctive features rely more on the geometry of the enclosure in small enclosures and rely more on the features in large enclosures. Here, these results are modeled using a recent associative model of geometry learning [Miller, N.Y., Shettleworth, S.J., 2007. Learning about environmental geometry: an associative model. J. Exp. Psychol. Anim. B 33, 191–212]. By adjusting the salience of either geometric or featural information or both the model is capable of reproducing much of the data on the effects of enclosure size on geometry learning.