XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry

XMapTools is a MATLAB©-based graphical user interface program for electron microprobe X-ray image processing, which can be used to estimate the pressure–temperature conditions of crystallization of minerals in metamorphic rocks. This program (available online at http://www.xmaptools.com) provides a method to standardize raw electron microprobe data and includes functions to calculate the oxide weight percent compositions for various minerals. A set of external functions is provided to calculate structural formulae from the standardized analyses as well as to estimate pressure–temperature conditions of crystallization, using empirical and semi-empirical thermobarometers from the literature. Two graphical user interface modules, Chem2D and Triplot3D, are used to plot mineral compositions into binary and ternary diagrams. As an example, the software is used to study a high-pressure Himalayan eclogite sample from the Stak massif in Pakistan. The high-pressure paragenesis consisting of omphacite and garnet has been retrogressed to a symplectitic assemblage of amphibole, plagioclase and clinopyroxene. Mineral compositions corresponding to ~165,000 analyses yield estimates for the eclogitic pressure–temperature retrograde path from 25 kbar to 9 kbar. Corresponding pressure–temperature maps were plotted and used to interpret the link between the equilibrium conditions of crystallization and the symplectitic microstructures. This example illustrates the usefulness of XMapTools for studying variations of the chemical composition of minerals and for retrieving information on metamorphic conditions on a microscale, towards computation of continuous pressure–temperature-and relative time path in zoned metamorphic minerals not affected by post-crystallization diffusion.

Composition Space Analysis in the Development of Copper Molybdate Hybrids Decorated by a Bifunctional Pyrazolyl/1,2,4-Triazole Ligand

A bitopic ligand, 4-(3,5-dimethylpyrazol-4-yl)-1,2,4-triazole (Hpz-tr) (1), containing two different heterocyclic moieties was employed for the design of copper(II)–molybdate solids under hydrothermal conditions. In the multicomponent CuII/Hpz-tr/MoVI system, a diverse set of coordination hybrids, [Cu(Hpz-tr)2SO4]·3H2O (2), [Cu(Hpz-tr)Mo3O10] (3), [Cu4(OH)4(Hpz-tr)4Mo8O26]·6H2O (4), [Cu(Hpz-tr)2Mo4O13] (5), and [Mo2O6(Hpz-tr)]·H2O (6), was prepared and characterized. A systematic investigation of these systems in the form of a ternary crystallization diagram approach was utilized to show the influence of the molar ratios of starting reagents, the metal (CuII and MoVI) sources, the temperature, etc., on the reaction products outcome. Complexes 2–4 dominate throughout a wide crystallization range of the composition triangle, while the other two compounds 5 and 6 crystallize as minor phases in a narrow concentration range. In the crystal structures of 2–6, the organic ligand behaves as a short [N–N]-triazole linker between metal centers Cu···Cu in 2–4, Cu···Mo in 5, and Mo···Mo in 6, while the pyrazolyl function remains uncoordinated. This is the reason for the exceptional formation of low-dimensional coordination motifs: 1D for 2, 4, and 6 and 2D for 3 and 5. In all cases, the pyrazolyl group is involved in H bonding (H-donor/H-acceptor) and is responsible for π–π stacking, thus connecting the chain and layer structures in more complicated H-bonding architectures. These compounds possess moderate thermal stability up to 250–300 °C. The magnetic measurements were performed for 2–4, revealing in all three cases antiferromagnetic exchange interactions between neighboring CuII centers and long-range order with a net moment below Tc of 13 K for compound 4.

RNA binding characteristics and overall topology of the vaccinia virus polyadenylation complex

mRNA 3′ polyadenylation is central to mRNA biogenesis in prokaryotes and eukaryotes, and is implicated in numerous aspects of mRNA metabolism, including efficiency of mRNA export from the nucleus, message stability, and initiation of translation. However, due to the great complexity of the eukaryotic polyadenylation apparatus, the mechanisms of RNA 3 ′ end processing have remained elusive. Although the RNA processing reactions leading to polyadenylated messenger RNA have been studied in many systems, and much progress has been made, a complete understanding of the biochemistry of the poly(A) polymerase enzyme is still lacking. My research uses Vaccinia virus as a model system to gain a better understanding of this complicated polyadenylation process, which consist of RNA binding, catalysis and polymerase translocation. ^ Vaccinia virus replicates in the cytoplasm of its host cell, so it must employ its own poly(A) polymerase (PAP), a heterodimer of two virus encoded proteins, VP55 and VP39. VP55 is the catalytic subunit, adding 30 adenylates to a non-polyadenylated RNA in a rapid processive manner before abruptly changing to a slow, non-processive mode of adenylate addition and dissociating from the RNA. VP39 is the stimulatory subunit. It has no polyadenylation catalytic activity by itself, but when associated with VP55 it facilitates the semi-processive synthesis of tails several hundred adenylates in length. ^ Oligonucleotide selection and competition studies have shown that the heterodimer binds a minimal motif of (rU)2 (N)25 U, the “heterodimer binding motif”, within an oligonucleotide, and its primer selection for polyadenylation is base-type specific. ^ Crosslinking studies using photosensitive uridylate analogs show that within a VP55-VP39-primer ternary complex, VP55 comes into contact with all three required uridylates, while VP39 only contacts the downstream uridylate. Further studies, using a backbone-anchored photosensitive crosslinker show that both PAP subunits are in close proximity to the downstream −10 to −21 region of 50mer model primers containing the heterodimer binding motif. This equal crosslinking to both subunits suggests that the dimerization of VP55 and VP39 creates either a cleft or a channel between the two subunits through which this region of RNA passes. ^ Peptide mapping studies of VP39 covalently crosslinked to the oligonucleotide have identified residue R107 as the amino acid in close proximity to the −10 uridylate. This helps us project a conceptual model onto the known physical surface of this subunit. In the absence of any tertiary structural data for VP55, we have used a series of oligonucleotide selection assays, as well as crosslinking, nucleotide transfer assays, and gel shift assays to gain insight into the requirements for binding, polyadenylation and translocation. Collectively, these data allow us to put together a comprehensive model of the structure and function of the polyadenylation ternary complex consisting of VP39, VP55 and RNA. ^

NHERF1 recruits the tumor suppressors PTEN and PHLPP to synergistically inhibit the PI-3K pathway

Glioblastoma multiforme is the most common form of brain cancer that presents patients with a poor prognosis that has remained unchanged over the past few decades. The tumor suppressor phosphatase PTEN antagonizes one of the major oncogenic pathways involved in the progression of glioblastoma, and is frequently deleted in this cancer type. Contrary to our expectations, we found that most glioblastoma cells expressing endogenous PTEN also harbor basal PI-3K/AKT activation mainly attributable to impaired PTEN membrane localization. This alteration correlated with a shift of the adaptor protein NHERF1, which contributes to PTEN membrane recruitment in normal cells, from the membrane to the cytoplasm. In cells expressing membrane-localized NHERF1, only simultaneous PTEN and NHERF1 depletion achieved AKT activation, suggesting the involvement of additional PI-3K/AKT suppressor regulated by NHERF1. We identified these novel interactors of NHERF1 as the PHLPP1 and PHLPP2 phosphatases. ^ NHERF1 directly interacted and recruited both PHLPP proteins to the membrane and, through both NHERF1 PDZ domains, assembled ternary complexes consisting of PTEN-NHERF1-PHLPP. Only simultaneous depletion of PTEN and PHLPP1 significantly activated AKT and increased proliferation in cells with membrane-localized NHERF1. Analysis of glioblastoma human tumors revealed frequent loss of membrane-localized NHERF1. On the other hand, targeting of NHERF1 to the membrane achieved suppression of AKT and cell proliferation. Our findings reveal a novel mechanism for PI-3K/AKT regulation by the synergistic cooperation between two important tumor suppressors, PTEN and PHLPP, via the scaffold protein NHERF1. ^

Mechanism of subunit interaction and DNA binding of the heterotrimeric CCAAT binding factor CBF

Many eukaryotic promoters contain a CCAAT element at a site close ($-$80 to $-$120) to the transcription initiation site. CBF (CCAAT Binding Factor), also called NF-Y and CP1, was initially identified as a transcription factor binding to such sites in the promoters of the Type I collagen, albumin and MHC class II genes. CBF is a heteromeric transcription factor and purification and cloning of two of the subunits, CBF-A and CBF-B revealed that it was evolutionarily conserved with striking sequence identities with the yeast polypeptides HAP3 and HAP2, which are components of a CCAAT binding factor in yeast. Recombinant CBF-A and CBF-B however failed to bind to DNA containing CCAAT sequences. Biochemical experiments led to the identification of a third subunit, CBF-C which co-purified with CBF-A and complemented the DNA binding of recombinant CBF-A and CBF-B. We have recently isolated CBF-C cDNAs and have shown that bacterially expressed purified CBF-C binds to CCAAT containing DNA in the presence of recombinant CBF-A and CBF-B. Our experiments also show that a single molecule each of all the three subunits are present in the protein-DNA complex. Interestingly, CBF-C is also evolutionarily conserved and the conserved domain between CBF-C and its yeast homolog HAP5 is sufficient for CBF-C activity. Using GST-pulldown experiments we have demonstrated the existence of protein-protein interaction between CBF-A and CBF-C in the absence of CBF-B and DNA. CBF-B on other hand, requires both CBF-A and CBF-C to form a ternary complex which then binds to DNA. Mutational studies of CBF-A have revealed different domains of the protein which are involved in CBF-C interaction and CBF-B interaction. In addition, CBF-A harbors a domain which is involved in DNA recognition along with CBF-B. Dominant negative analogs of CBF-A have also substantiated our initial observation of assembly of CBF subunits. Our studies define a novel DNA binding structure of heterotrimeric CBF, where the three subunits of CBF follow a particular pathway of assembly of subunits that leads to CBF binding to DNA and activating transcription. ^

Petrological parameters of sands and sandstones from DSDP and ODP holes in arc-related areas

Detrital modes for 524 deep-marine sand and sandstone samples recovered on circum-Pacific, Caribbean, and Mediterranean legs of the Deep Sea Drilling Project and the Ocean Drilling Program form the basis for an actualistic model for arc-related provenance. This model refines the Dickinson and Suczek (1979) and Dickinson and others (1983) models and can be used to interpret the provenance/tectonic history of ancient arc-related sedimentary sequences. Four provenance groups are defined using QFL, QmKP, LmLvLs, and LvfLvmiLvl ternary plots of site means: (1) intraoceanic arc and remnant arc, (2) continental arc, (3) triple junction, and (4) strike-slip-continental arc. Intraoceanic- and remnant-arc sands are poor in quartz (mean QFL%Q < 5) and rich in lithics (QFL%L > 75); they are predominantly composed of plagioclase feldspar and volcanic lithic fragments. Continental-arc sand can be more quartzofeldspathic than the intraoceanic- and remnant-arc sand (mean QFL%Q values as much as 10, mean QFL%F values as much as 65, and mean QmKP%Qm as much as 20) and has more variable lithic populations, with minor metamorphic and sedimentary components. The triple-junction and strike-slip-continental groups compositionally overlap; both are more quartzofeldspathic than the other groups and show highly variable lithic proportions, but the strike-slip-continental group is more quartzose. Modal compositions of the triple junction group roughly correlate with the QFL transitional-arc field of Dickinson and others (1983), whereas the strike-slip-continental group approximately correlates with their dissected-arc field.

Geochemistry and trace elements at DSDP Hole 78-543A

The upper part of the basaltic substratum of the Atlantic abyssal plain, approaching subduction beneath the Barbados Ridge and thus presumably beneath the Lesser Antilles island arc, is made of typical LREE-depleted oceanic tholeiites. Mineralogical (microprobe) and geochemical (X-ray fluorescence, neutron activation analyses) data are given for 12 samples from the bottom of Hole 543A, which is 3.5 km seaward of the deformation front of the Barbados Ridge complex. These basalts are overlain by a Quaternary to Maestrichtian-Campanian sedimentary sequence. Most of the basalts are relatively fresh (in spite of the alteration of olivine and development of some celadonite, clays, and chlorite in their groundmass), and their mineralogical and geochemical compositions are similar to those of LREE-depleted recent basalts from the Mid-Atlantic Ridge. The most altered samples occur at the top of the basaltic sequence, and show trends of enrichment in alkali metals typical of altered oceanic tholeiites.

Tie points and goechemical analysis from different Holes of ODP Site 165-1002

The fine-grained sediments of the Cariaco Basin, Venezuela, of the last 130 ky, whose deposition history is well characterized, were analyzed geochemically in order to test the validity of sediment bulk geochemistry as an indicator of detrital provenance. Several binary and ternary diagrams as well as the chemical index of alteration (CIA) were tested for their capacity to discriminate the poorly contrasted detrital sources to the Cariaco Basin, and to describe the temporal evolution of the contributions of these different sources. Most of the diagrams tested did not allow a good discrimination of sources or, when sources were well discriminated, did not allow an interpretation of the temporal variations consistent with the known history. A relatively good discrimination of sources and a consistent interpretation of temporal variations were however obtained using Hf vs. Th and La/Yb vs. Gd/Yb binary diagrams, as well as Ti-Zr-Th, Ti-Zr-La, and Lu-Hf-Th ternary diagrams. Compared to the previous studies of the detrital content of the Cariaco Basin sediments, the geochemical approach permitted the recognition of a sediment contribution eroded from the Unare platform and Gulf of Cariaco during rapid sea level oscillations, and the contribution of Saharan eolian particles during the Younger Dryas-Preboreal and MIS6-5 transition. The choice of plotted elements was determined after considering carrier minerals, so that different elements may be informative in different sedimentary contexts. Overall, mineral sorting during transport appears as a major limit to quantitative estimation of the different contributions. In particular mineral sorting leads to the selective enrichment of elements associated with clays (Al, Rb, Th and LREE) in sediments deposited in the basin. Unless the geochemical effect of mineral sorting can be measured, it appears that quantitative provenance analysis should be performed on fractions of similar grain size instead of bulk sediment.

Geochemistry of sediment cores from the Rainbow vent site

A geochemical investigation was carried out on two sediment cores collected at 2 and 5 km from the Rainbow hydrothermal vent site. Bulk sediment compositions indicate that these cores record clear enrichments in Fe, Cu, Mn, V, P and As from hydrothermal plume fallout (Cave et al., 2002, doi:10.1016/S0016-7037(02)00823-2). Sequential dissolution of the bulk sediments has been used to discriminate between a leach (biogenic and oxy-hydroxide) component and a residual phase (detrital and sulphide/sulphate fractions). Major element data (Al, Fe, Ti, Mn, Mg, Ca, Si and index%) reveal that the hydrothermal input, as recorded in the leach phase, is much stronger than apparent from bulk sediment analyses alone. REE patterns for the leach phase record contributions from both biogenic carbonate (mimicking seawater REE patterns) and hydrothermal oxy-hydroxides, with the latter exhibiting positive Eu anomalies (hydrothermal derived) and negative Ce anomalies (seawater derived). Based on major element and REE data, the residue contains contributions from aeolian dust input, local MORB material and a hydrothermal component. Ternary REE mixing calculations indicate that most of the REE within the residual fraction (~80%) is derived from hydrothermal material, while detrital contributions to the REE budget, as deep-sea clay and volcanic debris, are <20%. By combining bulk and REE data for the various end-member components of the residue, we calculate that the chemical composition of the residue hydrothermal end-member is high in Ca (6-15%) and with a Nd/Sr ratio of 0.004. These characteristics indicate the presence of low-solubility hydrothermal sulphate (rather than sulphide) material within the residue component of Rainbow hydrothermal sediments.

Sedimentology and geochemistry of ODP Leg 129 siliceous deposits

Siliceous deposits drilled on Ocean Drilling Program Leg 129 accumulated within a few degrees of the equator during the Jurassic through early Tertiary, as constrained by paleomagnetic data. During the Jurassic and Early Cretaceous, radiolarian ooze, mixed with a minor amount of pelagic clay, was deposited near the equator, and overall accumulation rates were moderate to low. At a smaller scale, in more detail, periods of relatively higher accumulation rates alternated with periods of very low accumulation rates. Higher rates are represented by radiolarite and limestone; lower rates are represented by radiolarian claystone. Our limited data from Leg 129 suggests that accumulation of biogenic deposits was not symmetrical about the equator or consistent over time. In the Jurassic, sedimentation was siliceous; in the Cretaceous there was significant calcareous deposition; in the Tertiary claystone indicates significantly lower accumulation rates at least the northern part of the equatorial zone. Accumulation rates for Leg 129 deposits in the Cretaceous were higher in the southern part of the equatorial zone than in the northern part, and the southern side of this high productivity zone extended to approximately 15°S, while the northern side extended only to about 5°N. Accumulation rates are influenced by relative contributions from various sediment sources. Several elements and element ratios are useful for discriminating sedimentary sources for the equatorial depositional environments. Silica partitioning calculations indicate that silica is dominantly of biogenic origin, with a detrital component in the volcaniclastic turbidite units, and a small hydrothermal component in the basal sediments on spreading ridge basement of Jurassic age at Site 801. Iron in Leg 129 sediments is dominantly of detrital origin, highest in the volcaniclastic units, with a minor hydrothermal component in the basal sediments at Site 801. Manganese concentrations are highest in the units with the lowest accumulation rates. Fe/Mn ratios are >3 in all units, indicating negligible hydrothermal influence. Magnesium and aluminum concentrations are highest in the volcaniclastic units and in the basal sediments at Site 801. Phosphorous is very low in abundance and may be detrital, derived from fish parts. Boron is virtually absent, as is typical of deep-water deposits. Rare earth element concentrations are slightly higher in the volcaniclastic deposits, suggesting a detrital source, and lower in the rest of the lithologic units. Rare earth element abundances are also low relative to "average shale." Rare earth element patterns indicate all samples are light rare earth element enriched. Siliceous deposits in the volcaniclastic units have patterns which lack a cerium anomaly, suggesting some input of rare earth elements from a detrital source; most other units have a distinct negative Ce anomaly similar to seawater, suggesting a seawater source, through adsorption either onto biogenic tests or incorporation into authigenic minerals for Ce in these units. The Al/(Al + Fe + Mn) ratio indicates that there is some detrital component in all the units sampled. This ratio plotted against Fe/Ti shows that all samples plot near the detrital and basalt end-members, except for the basal samples from Site 801, which show a clear trend toward the hydrothermal end-member. The results of these plots and the association of high Fe with high Mg and Al indicate the detrital component is dominantly volcaniclastic, but the presence of potassium in some samples suggests some terrigenous material may also be present, most likely in the form of eolian clay. On Al-Fe-Mn ternary plots, samples from all three sites show a trend from biogenic ooze at the top of the section downhole to oceanic basalt. On Si-Fe-Mn ternary plots, the samples from all three sites fall on a trend between equatorial mid-ocean spreading ridges and north Pacific red clay. Copper-barium ratios show units that have low accumulation rates plot in the authigenic field, and radiolarite and limestone samples that have high accumulation rates fall in the biogenic field.

Composition and structural formulas of ODP Site 200-1224 Eocene ferrobasalt minerals

The ~46-m.y.-old igneous basement cored during Leg 200 in the North Pacific represents one of the few cross sections of Pacific oceanic crust with a total penetration into basalt of >100 m. The rocks, emplaced during the Eocene at a fast-spreading rate (~14 cm/yr; full rate) are strongly differentiated tholeiitic basalts (ferrobasalts) with 7-4.5 wt% MgO, relatively high TiO2 (2-3.5 wt%), and total iron as Fe2O3 (9.1-16.8 wt%). The differentiated character of these lavas is related to unusually large amounts of crystallization differentiation of plagioclase, clinopyroxene, and olivine. The lithostratigraphy of the basement (cored to ~170 meters below seafloor) is divided into three units. The deepest unit (lithologic Unit 3), is a succession of lava flows of no more that a few meters thickness each. The intermediate unit (lithologic Unit 2) is represented by intermixed thin flows and pillows, whereas the shallowest unit (lithologic Unit 1), comprises two massive flows. The rocks range from aphyric to sparsely clinopyroxene-plagioclase-phyric (phenocryst content = <3 vol%) and from holocrystalline to hypohyaline. Chilled margins of pillow fragments show holohyaline to sparsely vitrophyric textures. Site 1224 oxide minerals present a type of alteration not previously seen, where titanomagnetite is only partially destroyed and the pure magnetite component is partially removed from the mineral, leaving, in the most extreme case, a nearly pure ulvöspinel residuum. As a result of this dissolution, iron, mainly in the oxidized state, is added to the circulating solvent fluids. This means that a considerable metal source can result from low-temperature reactions throughout the upper ocean crust. The coarsest-grained lithologic Unit 1 rocks have interstitial myrmekitic intergrowths of quartz and sodic plagioclase (~An12), roughly similar in mineralogy and bulk composition to tonalite/trondhjemite veinlets in abyssal gabbros from the southwest Indian Ocean and Hess Deep, eastern equatorial Pacific. Based on idiomorphic relationships and projections into the simplified Q-Ab-Or-H2O granite ternary system, the myrmekitic intergrowths formed at the same time as, or just after, the oxide minerals coprecipitated and at low water vapor pressure (~0.5 kbar). Their compositions correspond to SiO2-oligoclase intergrowths that are considerably less potassic than dacitic glasses that erupt, although rarely, along the East Pacific Rise or that have been produced experimentally by partial melting of gabbro. Based on the crystallization history and comparison to experimental data, the original interstitial siliceous liquids resulted from late-stage immiscible separation of siliceous and iron-rich liquids. The rare andesitic lavas found along the East Pacific Rise may be hybrid rocks formed by mixing of these immiscible siliceous melts with basaltic magma.

PanPlot - software to visualize profiles and core logs

The program PanPlot was developed as a visualization tool for the information system PANGAEA. It can be used as a stand-alone application to plot data versus depth or time or in a ternary view. Data input format is tab-delimited ASCII (e.g. by export from MS-Excel or from PANGAEA). The default scales and graphic features can individualy be modified. PanPlot graphs can be exported in platform-specific interchange formats (EMF, PICT) which can be imported by graphic software for further processing.

Deep levels in a-plane, high Mg-content MgxZn1-xO epitaxial layers grown by molecular beam epitaxy

Deep level defects in n-type unintentionally doped a-plane MgxZn1−xO, grown by molecular beam epitaxy on r-plane sapphire were fully characterized using deep level optical spectroscopy (DLOS) and related methods. Four compositions of MgxZn1−xO were examined with x = 0.31, 0.44, 0.52, and 0.56 together with a control ZnO sample. DLOS measurements revealed the presence of five deep levels in each Mg-containing sample, having energy levels of Ec − 1.4 eV, 2.1 eV, 2.6 V, and Ev + 0.3 eV and 0.6 eV. For all Mg compositions, the activation energies of the first three states were constant with respect to the conduction band edge, whereas the latter two revealed constant activation energies with respect to the valence band edge. In contrast to the ternary materials, only three levels, at Ec − 2.1 eV, Ev + 0.3 eV, and 0.6 eV, were observed for the ZnO control sample in this systematically grown series of samples. Substantially higher concentrations of the deep levels at Ev + 0.3 eV and Ec − 2.1 eV were observed in ZnO compared to the Mg alloyed samples. Moreover, there is a general invariance of trap concentration of the Ev + 0.3 eV and 0.6 eV levels on Mg content, while at least and order of magnitude dependency of the Ec − 1.4 eV and Ec − 2.6 eV levels in Mg alloyed samples.

Electronic, structural, and optical properties of the host and Cr-doped cadmium thioindate

The cadmium thioindate spinel CdIn2S4 semiconductor has potential applications for optoelectronic devices. We present a theoretical study of the structural and optoelectronic properties of the host and of the Cr-doped ternary spinel. For the host spinel, we analyze the direct or indirect character of the energy bandgap, the change of the energy bandgap with the anion displacement parameter and with the site cation distribution, and the optical properties. The main effect of the Cr doping is the creation of an intermediate band within the energy bandgap. The character and the occupation of this band are analyzed for two substitutions: Cr by In and Cr by Cd. This band permits more channels for the photon absorption. The optical properties are obtained and analyzed. The absorption coefficients are decomposed into contributions from the different absorption channels and from the inter-and intra-atomic components.

Electronic property analysis of O-doped Cu3SbS3

The ternary Cu-Sb-S semiconductors are considered to be sustainable and potential alternative absorber materials in thin film photovoltaic applications. In these compounds, several phases may coexist, albeit in different proportions depending on experimental growth conditions. Additionally, the photovoltaic efficiency could be increased with isoelectronic doping. In this work we analyze the electronic properties of O-doped Cu3SbS3 in two structures: the wittichenite and the skinnerite. We use first-principles within the density functional formalism with two different exchange-correlation potentials. In addition, we estimate the potential of these compounds for photovoltaic applications.