ALBERT

Description: DNA repair helicases function in the cell to separate DNA duplexes or remodel nucleoprotein complexes. These functions are influenced by sensing and signaling; the cellular pool of a DNA helicase may contain subpopulations of enzymes carrying different post-translational modifications and performing distinct biochemical functions. Here, we report a novel experimental strategy, single-molecule sorting, which overcomes difficulties associated with comprehensive analysis of heterologously modified pool of proteins. This methodology was applied to visualize human DNA helicase F-box–containing DNA helicase (FBH1) acting on the DNA structures resembling a stalled or collapsed replication fork and its interactions with RAD51 nucleoprotein filament. Individual helicase molecules isolated from human cells with their native post-translational modifications were analyzed using total internal reflection fluorescence microscopy. Separation of the activity trajectories originated from ubiquitylated and non-ubiquitylated FBH1 molecules revealed that ubiquitylation affects FBH1 interaction with the RAD51 nucleoprotein filament, but not its translocase and helicase activities.

Description: Dunite bands and dikes in ophiolitic mantle peridotites are interpreted as fossil melt channels within the suboceanic mantle. Concordant dunite bands (i.e. fossil melt channels transposed by outward transportation from the ridge axis via horizontal mantle flow) are particularly important as they possibly represent the melt channels through which the parental melts of mid-ocean ridge basalt (MORB) were transported to shallower depths beneath the paleo-ridge axis. We conducted field observations and sampling of concordant dunite bands (CDB) and their host harzburgite at selected outcrops covering a wide depth range in the mantle section along an inferred paleo-ridge segment in the northern to central part of the Oman ophiolite. The CDB increase in thickness and decrease in frequency upward. They are thicker and more frequent in the centre of the segment than near the segment ends when compared at the same stratigraphic level. The CDB consist mostly of olivine with minor spinel and very rare amounts of pyroxene. Clinopyroxene has a small grain size and an interstitial position relative to olivine. The constituent minerals in the CDB and their host harzburgite were analyzed by electron microprobe for major elements and by laser ablation inductively coupled plasma mass spectrometry for trace elements. Most of the CDB have refractory major element mineral compositions, such as high Fo [100 x Mg/(Mg + Fe)] in olivine (〉90·5), high Cr# [Cr/(Cr + Al)] in chromian spinel (〉0·50), and low Al 2 O 3 (〈3·5 wt %) in clinopyroxene. Chondrite-normalized trace element patterns of clinopyroxene in the host harzburgites consistently show a gentle decrease from heavy REE (HREE) to middle REE (MREE) and a sharp decrease from MREE to light REE (LREE) (= highly depleted), but those in the CDB show weaker LREE depletion, which is more variable depending on the stratigraphic level and position along the paleo-ridge segment. In contrast, the HREE concentrations in clinopyroxene in the CDB are higher than or similar to those of the host harzburgites. Trace element compositions of clinopyroxene in the CDB and their host harzburgites are evaluated with a one-dimensional, steady-state, open-system decompressional melting–reaction model. The modeling results suggest that an LREE-enriched melt generated at high pressure was transported upwards through melt channels to the shallow mantle (up to the Moho transition zone), where it mingled with highly depleted melts accumulated from fractionally melted peridotites to generate normal (N)-MORB-like melts. The mantle started upwelling (= melting) in the garnet stability field in the segment centre, but either in the garnet or in the spinel stability field near the segment ends. This suggests a variation of geothermal gradient along the paleo-ridge segment: higher in the segment centre and lower near the segment ends. This inference is supported by the presence of thicker (up to 250 cm) CDB as well as more frequent occurrence of CDB in the segment centre than near the segment end and by the geochemical evidence for chromatographic N-MORB-like melt percolation into the host peridotite only in the uppermost horizons near the segment ends.

Description: An accurate method using image sharpness to determine the best focusing is proposed for ultra-high-voltage electron microscopy. This method maximizes image sharpness for adjusting the focus. Five images with different defocus values are used to calculate the image sharpness. To obtain the best focus value that produces greatest image sharpness, fitting the quasi-Gaussian function to five image sharpness is a suitable alternative. This method, which maximizes image sharpness, gives better accuracy than the wobbler method for the ultra-high-voltage electron microscope. The focusing area can be selected without moving the field of view, because the focusing area can be selected at almost any area in the image.

Description: Major and trace element and Sr–Nd–Pb isotope data for whole-rocks and major element data for minerals within basalt samples from the Chugaryeong volcano, an intra-plate back-arc volcanic centre in the central part of the Korean Peninsula, are used to address the process of magma genesis in the deep back-arc region of eastern Asia. There are two lava flow units at Chugaryeong volcano: the Chongok (0·50 Ma) and the Chatan (0·15 Ma) basalts. These basalts have similar MgO (9·1–10·4 wt %) but exhibit differences in their major and trace element and isotope compositions. The Chongok basalt has higher TiO 2 , Al 2 O 3 , Na 2 O, K 2 O, P 2 O 5 , Cr 2 O 3 , large ion lithophile elements (LILE), high field strength elements (HFSE), and rare earth elements (REE), and lower FeO*, SiO 2 , and CaO than the Chatan basalt. In addition, the Chongok basalt has more radiogenic 143 Nd/ 144 Nd and 206 Pb/ 204 Pb, and less radiogenic 87 Sr/ 86 Sr and 208 Pb/ 204 Pb than the Chatan basalt. Chi-square tests for the major elements indicate that crystal fractionation can explain the chemical variations within each basalt suite; intra-crustal processes, including crystal fractionation and assimilation of continental crust, cannot result in the formation of one basalt suite from the other. The Sr–Nd–Pb isotopic compositions of the Chongok and Chatan basalts plot on mixing hyperbolae between peridotite mantle xenoliths from the area and a fluid flux derived from a mixture of ancient and recent sediments. The trace element compositions of the estimated primary melts for the two basalt suites suggest different degrees of partial melting of a common enriched mantle source that was metasomatized by a Ba-, K-, Pb-, and Sr-rich fluid. The estimated degree of melting increased with time from ~7·5% for the Chongok basalt to ~10% for the Chatan basalt. The source mantle for the Chatan basalt is more enriched in Ba and Pb, indicating a greater fluid flux than for the Chongok basalt. This suggests that melting of the source mantle increased with time, sustained by an increased sediment-derived fluid flux from the deeper upper mantle.

Description: The mechanism of fractionation in a sheet-like magma body was investigated based on observations from the Nosappumisaki intrusion, northern Japan. This is one of a number of late Cretaceous shoshonite sills in the Nemuro peninsula and has a compound structure comprising a bottom cumulate zone containing ~50 vol. % cumulus crystals and a overlying middle zone free of such cumulus crystals. These zones are sandwiched between porphyritic rocks of upper and lower chilled and marginal zones. It is inferred that massive crystal settling or flotation from a magma initially laden with ~20 vol. % of crystals (primocrysts) in a sheet-like magma body formed a cumulus pile and an overlying crystal-free melt layer. After the formation of the compound structure with partial freezing of the upper and lower marginal zones, the internal part of the intrusion slowly solidified. During this period the melt in the central part of the intrusive sheet underwent fractional crystallization. This is shown by patterns of vertical variation in the composition of the interstitial melt. The overall patterns are inverted (mirror-image) S-shaped and S-shaped for incompatible and compatible elements, respectively. The incompatible element abundances show maxima near the bottom of the middle zone, which corresponds to the final solidification horizon. They show minima in the cumulate zone, which suggests discharge of an evolved melt from the crystal pile. Fractionation is inferred to have taken place via compositional convection without settling of crystals grown after the intrusion event or collapse of the upper boundary layer. The melt in the central melt layer descended into the permeable crystal pile counterbalancing discharge of buoyant evolved melt formed by crystallization of the pore melt in the crystal pile. This conclusion is based on the following observations. (1) There is no accumulation of crystals grown after the intrusion of the magma above the cumulate zone. (2) Leucocratic pipe-like structures, which represent relict pathways for the evolved melt, are developed in the cumulate zone. These structures increase in diameter, decrease in number density, and increase in abundance of incompatible elements with height. (3) Cumulus augite in the cumulate zone has Ca-rich and Al-poor dissolved rims. The extent of dissolution increases with stratigraphic height, suggesting downwelling of an H 2 O-rich melt from the overlying melt layer. (4) There is no evidence for extensive compaction accompanying pore melt crystallization in the main part of the cumulate zone. (5) The initial melt composition estimated from the groundmass of the chilled margin rocks and the average composition of the material interstitial to the primocrysts for the whole sill are statistically identical. A mass-balance model for compositional convection was constructed to quantify the melt transportation processes. Model parameters were optimized by fitting the observed vertical variation of the interstitial melt compositions. The optimized results suggest that the evolved melts discharged from the crystal pile and rose through the central melt layer as plumes with minor mingling with the surrounding melt. The initially formed compound structure is a highly preferential environment for compositional convection.

Description: Intra-plate Cenozoic volcanism in Kita-Matsuura, northwestern Kyushu, Japan, shows systematic spatio-temporal changes in geochemistry that can be explained by partial melting followed by melt segregation in a region of upwelling mantle. We have examined the thermal and melting history of the upwelling mantle by quantitatively estimating melt water contents and melting conditions. The water content of a spectrum of primary melts is estimated to range from 0·5 to 1·5 wt % based on a combination of a plagioclase-liquid and olivine-saturated liquid geohygrometers and MELTS calculations. The estimated melt segregation temperature ranges from 1330 to 1500°C, at pressures from 1·7 to 2·8 GPa under hydrous conditions. Melting temperature and pressure decreased with time, whereas the water content of the primary melts increased. Corresponding temporal decreases in high field strength element (HFSE) abundances and HFSE/large ion lithophile element (LILE) ratios require progressive melt extraction and aggregation from a melting mantle with a continuous and gradually increasing input of H 2 O-rich fluid or melt into the melting system. The estimated isotope composition of influxed fluid lies on a mixing line between the sediment and altered oceanic crust of the Philippine Sea Plate, with strong affinity to the sediment composition. Based on the temporal variation of the magmas and the melting model, we propose small-scale upwelling ( c. 70 km in diameter) of a dry mantle peridotite that interacts progressively with the overlying wet mantle wedge. The wet mantle wedge was previously hydrated by fluids from sediments from the subducted Philippine Sea Plate, whereas the deep and dry mantle could have been derived from the mantle beneath the subducted Pacific Plate through a slab window.

Description: We show that there exists an infinite family of knots, each of which has, for each integer $k\geq 0$ , a destabilized $(2k+5)$ -bridge sphere. We also show that, for each integer $n\geq 4$ , there exists a knot with a destabilized 3-bridge sphere and a destabilized $n$ -bridge sphere.

Description: During the repair of articular cartilage, type I collagen (COL1)-based fibrous tissues change into a mixture of COL1 and type II collagen (COL2) and finally form hyaline cartilaginous tissues consisting of COL2. In order to elucidate the changes that occur in the matrix during cartilage repair and the roles of fibroblasts and chondrocytes in this process, we generated a minimal cartilage defect model that could be spontaneously repaired. Defects of 0.3 mm were created on the patellofemoral articular cartilage of rats using an Er:YAG laser and were observed histologically, ultrastructurally and histochemically. At week 2 after this operation, fibroblastic cells were found to be surrounded by COL1 throughout the area of the defect. These cells became acid phosphatase positive by week 4, both taking in and degrading collagen fibrils. Thereafter, the cells became rounded, with both COL1 and 2 evident in the matrix, and showed immunolocalized matrix metalloproteinase-1 or -9. In the region of the bone marrow, the cells became hypertrophic and were surrounded mainly by COL2 and proteoglycans. By the eighth week, the cartilaginous matrix was found to contain abundant COL2, in which collagen fibrils of various diameters were arranged irregularly. These morphological changes suggested that the fibroblastic cells both produce and resolve the matrix and undertake remodeling to become chondrocytes by converting from a COL1- into a COL2-dominant matrix. This process eventually forms new articular cartilage, but this is not completely identical to normal articular cartilage at the ultrastructural level.

Description: A complex of the three ( α ) core subunits and the β 2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of (proofreading exonuclease) subunits shows that is attached to α at a site far from the polymerase active site. Both α and contain clamp-binding motifs (CBMs) that interact simultaneously with β 2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable α : β 2 complexes. Nuclear magnetic resonance experiments with reconstituted α : β 2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of with its α -binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p -benzoyl-L-phenylalanine incorporated at different sites in the α -PHP domain confirm the conformational variability of the tether. Structural models of the α : β 2 replicase complex with primer-template DNA combine all available structural data.

Description: Galectins are a group of animal lectins characterized by their specificity for β-galactosides. Mouse galectin-2 (mGal-2) is predominantly expressed in the gastrointestinal tract and has been identified as one of the main gastric mucosal proteins that are uniquely sensitive to S-nitrosylation. We have previously reported that oxidation of mGal-2 by hydrogen peroxide (H 2 O 2 ) resulted in the loss of sugar-binding ability, whereas pre-treatment of mGal-2 with S-nitrosocysteine prevented H 2 O 2 -induced inactivation. In this study, we used point-mutated recombinant mGal-2 proteins to study which of the two highly conserved Cys residues in mGal-2 must be S-nitrosylated for protection against oxidative inactivation. Mutation of Cys 57 to a Met residue (C57M) did not result in lectin inactivation following H 2 O 2 treatment, whereas Cys 75 mutation to Ser (C75S) led to significantly reduced lectin activity, as is the case for wild-type mGal-2. However, pre-treatment of the C75S mutant with S-nitrosocysteine protected the protein from H 2 O 2 -induced inactivation. Therefore, Cys 57 is suggested to be responsible for oxidative inactivation of the mGal-2 protein, and protection of the sulfhydryl group of the Cys 57 in mGal-2 by S-nitrosylation is likely important for maintaining mGal-2 protein function in an oxidative environment such as the gastrointestinal tract.