The genome of Rhizobium leguminosarum has recognizable core and accessory components

Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alpha A-, alpha beta- and R120G alpha B-Crystallins

alpha B-Crystallin is a ubiquitous small heat-shock protein (sHsp) renowned for its chaperone ability to prevent target protein aggregation. It is stress-inducible and its up-regulation is associated with a number of disorders, including those linked to the deposition of misfolded proteins, such as Alzheimer's and Parkinson's diseases. We have characterised the formation of amyloid fibrils by human alpha B-crystallin in detail, and also that of alpha A-crystallin and the disease-related mutant R120G (alpha B-crystallin. We find that the last 12 amino acid residues of the C-terminal region of alpha B-crystallin are predicted from their physico-chemical properties to have a very low propensity to aggregate. H-1 NMR spectroscopy reveals that this hydrophilic C-terminal region is flexible both in its solution state and in amyloid fibrils, where it protrudes from the fibrillar core. We demonstrate, in addition, that the equilibrium between different protofilament assemblies can be manipulated and controlled in vitro to select for particular alpha B-crystallin amyloid morphologies. Overall, this study suggests that there could be a fine balance in vivo between the native functional sHsp state and the formation of amyloid fibrils. (C) 2007 Elsevier Ltd. All rights reserved.

Fracture resistance of endodontically treated teeth with different heights of crown ferrule restored with prefabricated carbon fiber post and composite resin core by intermittent loading

This study evaluated the fracture resistance of endodontically treated teeth restored with prefabricated carbon fiber posts and varying quantities of coronal dentin. Sixty freshly extracted upper canines were randomly divided into groups of 10 teeth each. The specimens were exposed to 250,000 cycles in a controlled chewing simulator. All intact specimens were subjected to a static load (N) in a universal testing machine at 45 degrees to the long axis. Data were analyzed by 1-way analysis of variance and Tukey test (alpha = .05). Significant differences (P < .001) were found among the mean fracture forces of the test groups (positive control, 0 mm, 1 mm, 2 mm, 3 mm, and negative control groups: 1022.82 N, 1008.22 N, 1292.52 N, 1289.19 N, 1255.38 N, and 1582.11, respectively). These results suggested that the amount of coronal dentin did not significantly increase the fracture resistance of endodontically treated teeth restored with prefabricated carbon fiber post and composite resin core. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2008;106:e52-e57)

Iron Oxide Versus Fe55Pt45/Fe3O4: Improved Magnetic Properties of Core/Shell Nanoparticles for Biomedical Applications

In this paper, synthesis of the Fe55Pt45/Fe3O4 core/shell structured nanoparticles using the modified polyol process combined with the seed-mediated growth method is reported. Iron oxide shell thickness was tuned controlling the Fe(acac)(3)/FePt seeds in the reaction medium. Annealing of the core/shell structure leads to iron-rich layer formation around the hard FePt phase in the nanoparticle core. However, the 2 nm Fe3O4 shell thickness seems to be the limit to obtain the enhanced magnetization close to the alpha-Fe and preserving an iron oxide shell after annealing at 500 degrees C for 30 min in a reducing atmosphere. The presence of both the oxide layer on nanoparticle surface and an intermediate iron-rich FePt layer after annealing promote strong decreases in the coercive field of the 2-nm-oxide shell thickness. These annealed nanoparticles were functionalized with dextran, presenting the enhanced characteristics for biomedical applications such as higher magnetization, very low coercivity, and a slightly iron oxide passivated layer, which leads an easy functionalization and decreases the nanoparticle toxicity.

Charge distribution and calcium affinity of sulfated alpha-L-galactans from ascidians. Comparison between linear and highly branched polymers

Calcium binding and charge distribution on highly branched and linear sulfated L-galactans from ascidians have been studied using a metallochromic indicator and conductimetric titrations. The distance between charged groups of the linear and highly branched galactans does not vary despite their marked differences in sulfate/total sugar molar ratios. These results indicate that the sulfated L-galactose units are concentrated in the central polysaccharide core and not intercalated among non-sulfated units. This inference is consistent with the chemical studies of these galactans. Surprisingly, calcium affinity increases with increasing amounts of non-sulfated sugar branches in the molecule. Thus, calcium binding in these polymers is not a simple function of availability of anion binding sites but a more complex calcium-polysaccharide interaction. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Interfacial photoluminescence emission properties of core/shell Al2O3/ZrO2

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of Surface Conditioning Modalities on the Repair Bond Strength of Resin Composite to the Zirconia Core / Veneering Ceramic Complex

Purpose: This study evaluated the effect of different surface conditioning protocols on the repair strength of resin composite to the zirconia core / veneering ceramic complex, simulating the clinical chipping phenomenon.Materials and Methods: Forty disk-shaped zirconia core (Lava Zirconia, 3M ESPE) (diameter: 3 mm) specimens were veneered circumferentially with a feldspathic veneering ceramic (VM7, Vita Zahnfabrik) (thickness: 2 mm) using a split metal mold. They were then embedded in autopolymerizing acrylic with the bonding surfaces exposed. Specimens were randomly assigned to one of the following surface conditioning protocols (n = 10 per group): group 1, veneer: 4% hydrofluoric acid (HF) (Porcelain Etch) + core: aluminum trioxide (50-mu m Al2O3) + core + veneer: silane (ESPE-Sil); group 2: core: Al2O3 (50 mu m) + veneer: HF + core + veneer: silane; group 3: veneer: HF + core: 30 mu m aluminum trioxide particles coated with silica (30 mu m SiO2) + core + veneer: silane; group 4: core: 30 mu m SiO2 + veneer: HF + core + veneer: silane. Core and veneer ceramic were conditioned individually but no attempt was made to avoid cross contamination of conditioning, simulating the clinical intraoral repair situation. Adhesive resin (VisioBond) was applied to both the core and the veneer ceramic, and resin composite (Quadrant Posterior) was bonded onto both substrates using polyethylene molds and photopolymerized. After thermocycling (6000 cycles, 5 degrees C-55 degrees C), the specimens were subjected to shear bond testing using a universal testing machine (1 mm/min). Failure modes were identified using an optical microscope, and scanning electron microscope images were obtained. Bond strength data (MPa) were analyzed statistically using the non-parametric Kruskal-Wallis test followed by the Wilcoxon rank-sum test and the Bonferroni Holm correction (alpha = 0.05).Results: Group 3 demonstrated significantly higher values (MPa) (8.6 +/- 2.7) than those of the other groups (3.2 +/- 3.1, 3.2 +/- 3, and 3.1 +/- 3.5 for groups 1, 2, and 4, respectively) (p < 0.001). All groups showed exclusively adhesive failure between the repair resin and the core zirconia. The incidence of cohesive failure in the ceramic was highest in group 3 (8 out of 10) compared to the other groups (0/10, 2/10, and 2/10, in groups 1, 2, and 4, respectively). SEM images showed that air abrasion on the zirconia core only also impinged on the veneering ceramic where the etching pattern was affected.Conclusion: Etching the veneer ceramic with HF gel and silica coating of the zirconia core followed by silanization of both substrates could be advised for the repair of the zirconia core / veneering ceramic complex.

Evaluation of tensile tetention of Y-TZP crowns after long-term aging: Effect of the core substrate and crown surface conditioning

This study evaluated the effect of the core substrate type (dentin and composite resin) on the retention of crowns made of yttrium oxide stabilized tetragonal zirconia polycrystal (Y-TZP), submitted to three inner surface conditionings. For this purpose, 72 freshly extracted molars were embedded in acrylic resin, perpendicular to the long axis, and prepared for full crowns: 36 specimens had crown preparations in dentin; the remaining 36 teeth had the crowns removed, and crown preparations were reconstructed with composite resin plus fiber posts with dimensions identical to the prepared dentin. The preparations were impressed using addition silicone, and 72 Y-TZP copings for the tensile test were produced. Cementation was performed with a dual-cured cement containing phosphate monomers. For cementation, the crown preparation (dentin or resin) was conditioned with the adhesive system, and the ceramic was subjected to one of three surface treatments: isopropyl alcohol, tribochemical silica coating, or thin low-fusing glassy porcelain layer application plus silanization. After 24 hours, all specimens were submitted to thermocycling (6000 cycles) and placed in a special tensile testing device in a universal testing machine to determine failure loads. The failure modes of all samples were analyzed under a stereomicroscope. Two-way analysis of variance showed that the surface treatment and substrate type (alpha=0.05) affected the tensile retention results. The dentin substrate presented the highest tensile retention values, regardless of the surface treatment. When the substrate was resin, the tribochemical silica coating and low-fusing glaze application plus silanization groups showed the higher retention values.

Effect of composite surface treatment and aging on the bond strength between a core build-up composite and a luting agent

Objective: The purpose of this study was to assess the influence of conditioning methods and thermocycling on the bond strength between composite core and resin cement. Material and Methods: Eighty blocks (8x8x4 mm) were prepared with core build-up composite. The cementation surface was roughened with 120-grit carbide paper and the blocks were thermocycled (5,000 cycles, between 5 degrees C and 55 degrees C, with a 30 s dwell time in each bath). A layer of temporary luting agent was applied. After 24 h, the layer was removed, and the blocks were divided into five groups, according to surface treatment: (NT) No treatment (control); (SP) Grinding with 120-grit carbide paper; (AC) Etching with 37% phosphoric acid; (SC) Sandblasting with 30 mm SiO2 particles, silane application; (AO) Sandblasting with 50 mu m Al2O3 particles, silane application. Two composite blocks were cemented to each other (n=8) and sectioned into sticks. Half of the specimens from each block were immediately tested for microtensile bond strength (mu TBS), while the other half was subjected to storage for 6 months, thermocycling (12,000 cycles, between 5 degrees C and 55 degrees C, with a dwell time of 30 s in each bath) and mu TBS test in a mechanical testing machine. Bond strength data were analyzed by repeated measures two-way ANOVA and Tukey test (alpha=0.05). Results: The mu TBS was significantly affected by surface treatment (p=0.007) and thermocycling (p=0.000). Before aging, the SP group presented higher bond strength when compared to NT and AC groups, whereas all the other groups were statistically similar. After aging, all the groups were statistically similar. SP submitted to thermocycling showed lower bond strength than SP without thermocycling. Conclusion: Core composites should be roughened with a diamond bur before the luting process. Thermocycling tends to reduce the bond strength between composite and resin cement.

The alpha-cluster model applied to 74Ge.

There are few studies using cluster models in the nuclei around the intermediate and heavy mass regions. The alpha-cluster model is based on the interaction between an alpha particle and a nucleus chosen as a core. This model can be applied to nuclear system where alpha-cluster stability is expected and the application in light and intermediate mass nuclei was able to give consistent descriptions of experimental data.

Stable isotopes of foraminifers, mineralogy and ages of sediment core GeoB1523-1

Today the western tropical Atlantic is the most important passage for cross-equatorial transfer of heat in the form of warm surface water flowing from the South into the North Atlantic. Circulation changes north of South America may thus have influenced the global thermohaline circulation system and high northern latitude climate. Here we reconstruct late Quaternary variations of western equatorial Atlantic surface circulation and Amazon lowland climate obtained from a multiproxy sediment record from Ceará Rise. Variations in the illite/smectite ratio suggest drier climatic conditions in the Amazon Basin during glacials relative to interglacials. The 230Thex-normalized fluxes and the 13C/12C record of organic carbon indicate that sea level fluctuations, shelf topography, and changes of the surface circulation pattern controlled variations and amplitude of terrigenous sediment supply to the Ceará Rise. We attribute variations in thermocline depth, reconstructed from vertical planktic foraminiferal oxygen isotope gradients and abundances of the phytoplankton species Florisphaera profunda, to changes in southeast trade wind intensity. Strong trade winds during ice volume maxima are associated with a deep western tropical Atlantic thermocline, strengthening of the North Brazil Current retroflection, and more vigorous eastward flow of surface waters.

Physical properties and sedimentology on core GeoB1510-1

Detailed information about the sediment properties and microstructure can be provided through the analysis of digital ultrasonic P wave seismograms recorded automatically during full waveform core logging. The physical parameter which predominantly affects the elastic wave propagation in water-saturated sediments is the P wave attenuation coefficient. The related sedimentological parameter is the grain size distribution. A set of high-resolution ultrasonic transmission seismograms (ca. 50-500 kHz), which indicate downcore variations in the grain size by their signal shape and frequency content, are presented. Layers of coarse-grained foraminiferal ooze can be identified by highly attenuated P waves, whereas almost unattenuated waves are recorded in fine-grained areas of nannofossil ooze. Color-encoded pixel graphics of the seismograms and instantaneous frequencies present full waveform images of the lithology and attenuation. A modified spectral difference method is introduced to determine the attenuation coefficient and its power law a = kfn. Applied to synthetic seismograms derived using a "constant Q" model, even low attenuation coefficients can be quantified. A downcore analysis gives an attenuation log which ranges from ca. 700 dB/m at 400 kHz and a power of n = 1-2 in coarse-grained sands to few decibels per meter and n ? 0.5 in fine-grained clays. A least squares fit of a second degree polynomial describes the mutual relationship between the mean grain size and the attenuation coefficient. When it is used to predict the mean grain size, an almost perfect coincidence with the values derived from sedimentological measurements is achieved.

Sedimentology and Th, Pa, U, and N isotopic composition of core MD84-527

High-resolution records of opal, carbonate, and terrigenous fluxes have been obtained from a high-sedimentation rate core (MD84-527: 43°50'S; 51°19'E; 3269 m) by normalization to 230Th. This method estimates paleofluxes to the seafloor on a point-by-point basis and distinguishes changes in sediment accumulation due to variations in vertical rain rates from those due to changes in syndepositional sediment redistribution by bottom currents. We also measured sediment delta15N to evaluate the changes in nitrate utilization in the overlying surface waters associated with paleoflux variations. Our results show that opal accumulation rates on the seafloor during the Holocene and stage 3, based on 14C dating, were respectively tenfold and fivefold higher than the vertical rain rates, At this particular location, changes in opal accumulation on the seafloor appear to be mainly controlled by sediment redistribution by bottom currents rather than variations in opal fluxes from the overlying water column. Correction for syndepositional sediment redistribution and the improved time resolution that can be achieved by normalization to 230Th disclose important variations in opal rain rates. We found relatively high but variable opal paleoflux during stage 3, with two maxima centered at 36 and 30 kyr B.P., low opal paleoflux during stage 2 and deglaciation and a pronounced maximum during the early Holocene, We interpret this record as reflecting variations in opal production rates associated with climate-induced latitudinal migration of the southern ocean frontal system. Sediments deposited during periods of high opal paleoflux also have high authigenic U concentrations, suggesting more reducing conditions in the sediment, and high Pa-231/Th-230 ratios, suggesting increased scavenging from the water column. Sediment delta15N is circa 1.5 per mil higher during isotopic stage 2 and deglaciation. The low opal rain rates recorded during that period appear to have been associated with increased nitrate depletion. This suggests that opal paleofluxes do not simply reflect latitudinal migration of the frontal system but also changes in the structure of the upper water column. Increased stratification during isotopic stage 2 and deglaciation could have been produced by a meltwater lid, leading to lower nitrate supply rates to surface waters.

Diatom abundances in sediment core CESAR_83-006

The modern Arctic Ocean is regarded as a barometer of global change and amplifier of global warming (Graversen et al., 2008, doi:10.1038/nature06502) and therefore records of past Arctic change are critical for palaeoclimate reconstruction. Little is known of the state of the Arctic Ocean in the greenhouse period of the Late Cretaceous epoch (65-99 million years ago), yet records from such times may yield important clues to Arctic Ocean behaviour in near-future warmer climates. Here we present a seasonally resolved Cretaceous sedimentary record from the Alpha ridge of the Arctic Ocean. This palaeo-sediment trap provides new insight into the workings of the Cretaceous marine biological carbon pump. Seasonal primary production was dominated by diatom algae but was not related to upwelling as was previously hypothesized (Kitchell and Clark, 1982, doi:10.1016/0031-0182(82)90087-6). Rather, production occurred within a stratified water column, involving specially adapted species in blooms resembling those of the modern North Pacific subtropical gyre (Dore et al., 2008, doi:10.1016/j.pocean.2007.10.002), or those indicated for the Mediterranean sapropels (Kemp et al., 1999, doi:10.1038/18001). With increased CO2 levels and warming currently driving increased stratification in the global ocean (Sarmiento et al., 1998, doi:10.1038/30455), this style of production that is adapted to stratification may become more widespread. Our evidence for seasonal diatom production and flux testify to an ice-free summer, but thin accumulations of terrigenous sediment within the diatom ooze are consistent with the presence of intermittent sea ice in the winter, supporting a wide body of evidence for low temperatures in the Late Cretaceous Arctic Ocean (Falcon-Lang et al., 2004, doi:10.1016/j.palaeo.2004.05.016; Amiot et al., 2004, doi:10.1016/j.epsl.2004.07.015; Otto-Bliesner et al., 2002, doi:10.1029/2001JD000821), rather than recent suggestions of a 15 °C mean annual temperature at this time (Jenkyns et al., 2004, doi:10.1038/nature03143).

Carbon uptake rate calculated for sea-ice core samples during POLARSTERN cruise ARK-XXVII/3 (IceArc) in 2012

Net Primary Production was measured using the 14**C uptake method with minor modifications. Melted sea ice samples were spiked with 0.1µCi ml**-1 of 14**C labelled sodium bicarbonate (Moravek Biochemicals, Brea, USA) and distributed in 10 clear bottles (20 ml each). Subsequently they were incubated for 12 h at -1.3°C under different scalar irradiances (0-420 µmol photons m**-2 s**-1) measured with a spherical sensor (Spherical Micro Quantum Sensor US-SQS/L, Heinz Walz, Effeltrich, Germany). At the end of the incubation, samples were filtered onto 0.2 µm nitrocellulose filters and the particulate radioactive carbon uptake was determined by liquid scintillation counting using Filter count scintillation cocktail (Perkin Elmer, Waltham, USA). The carbon uptake values in the dark were subtracted from the carbon uptake values measured in the light incubations. Dissolved inorganic carbon (DIC) was measured for each sample using the flow injection system (Hall and Aller, 1992). The DIC concentration was taken into account to calculate the amount of labeled bicarbonate incorporated into the cell. Carbon fixation rates were normalized volumetrically and by chlorophyll a. Photosynthesis-irradiance curves (PI curves) were fitted using MATLAB® according to the equation proposed by Platt et al. (1980) including a photoinhibition parameter (beta) and providing the main photosynthetic parameters: maximum Chla normalized carbon fixation rate if there were no photoinhibition (Pb) and the initial slope of the saturation curve (alpha). The derived parameters: light intensity at which photosynthesis is maximal (Im), the carbon fixation rate at that maximal irradiance (Pbm) and the adaptation parameter or photoacclimation index (Ik) were calculated according to Platt et al. (1982).