Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Absolute Thellier paleointensities from Ponta Grossa dikes (southern Brazil) and the early Cretaceous geomagnetic field strength

We report a detailed rock magnetic and Thellier paleointensity study from similar to 130.5 Ma Ponta Grossa Dike Swarms in Southern Brazil. Twenty-nine samples from seven cooling units were pre-selected for paleointensity experiments based on their low viscosity index, stable remanent magnetization and close to reversible continuous thermomagnetic curves. 19 samples characterized by negative pTRM tests, Arai concave- up curves or positive pTRM tests with NRM loss uncorrelated with TRM acquisition were rejected. High quality reliable paleointensity determinations are determined from detailed evaluation criteria, with 10 samples belonging to three dikes passing the tests. The site-mean paleointensity values obtained in this study range from 25.6 +/- 4.3 to 11.3 +/- 2.1 mu T and the corresponding VDM`s range from 5.7 +/- 0.9 to 2.5 +/- 0.5 (10(22) Am(2)). These data yield a VDM mean value of 4.1 +/- 1.6 x 10(22) Am(2). Significant variability of Earth`s magnetic field strength is observed for Ponta Grossa Dikes with the mean value being significantly lower as compared to the mean VDM obtained from the nearby Parana Magmatic Province. The paleointensities for the Ponta Grossa Dikes are in agreement with absolute paleointensities retrieved from the submarine basaltic glasses from 130 to 120 Ma. It seems that a relatively low field prevailed just before the Cretaceous Normal Superchron.

Verifiable Visualization for Isosurface Extraction

Visual representations of isosurfaces are ubiquitous in the scientific and engineering literature. In this paper, we present techniques to assess the behavior of isosurface extraction codes. Where applicable, these techniques allow us to distinguish whether anomalies in isosurface features can be attributed to the underlying physical process or to artifacts from the extraction process. Such scientific scrutiny is at the heart of verifiable visualization - subjecting visualization algorithms to the same verification process that is used in other components of the scientific pipeline. More concretely, we derive formulas for the expected order of accuracy (or convergence rate) of several isosurface features, and compare them to experimentally observed results in the selected codes. This technique is practical: in two cases, it exposed actual problems in implementations. We provide the reader with the range of responses they can expect to encounter with isosurface techniques, both under ""normal operating conditions"" and also under adverse conditions. Armed with this information - the results of the verification process - practitioners can judiciously select the isosurface extraction technique appropriate for their problem of interest, and have confidence in its behavior.

Boron isotope composition of tourmalinite and vein tourmalines associated with gold mineralization, Serra do Itaberaba Group, central Ribeira Belt, SE Brazil

Important concentrations of tourmaline occur as gold-bearing stratiform tourmalinites and in mineralized quartz-tourmaline veins at the Tapera Grande and Quartzito gold prospects in the Mesoproterozoic Serra do Itaberaba Group, central Ribeira Belt (Sao Paulo State, SE Brazil). The main rock types in both prospects constitute the volcanic-sedimentary Morro da Pedra Preta Formation, which formed in a submarine back-arc setting. At Tapera Grande, the volcanic-sedimentary sequence is composed of metabasic and metavolcaniclastic rocks, graphitic and sulfur-rich metapelites, banded iron formation, metandesite, metarhyolite, calcsilicates, tourmalinites and metahydrothermalites derived from mafic and felsic rocks. The Mesoproterozoic rocks at Quartzito prospect are lithologically similar but they have been affected by Neoproterozoic faulting and shearing and by the emplacement of granitic rocks, resulting in the formation of tourmaline-rich quartz-carbonate veins with gold and base metal mineralization. We conducted a chemical and B-isotope study of tourmalines in order to better understand the origin of the stratiform tourmalinites in the Morro da Pedra Preta Formation and their relationship with gold mineralization. The overall range of delta(11)B values obtained for the tourmalinite and vein tourmalines is between - 15%. and -5 parts per thousand, with the tourmalinites failing at the low end of this range (-15 to -8 parts per thousand). Such values are typical for continental crust and inconsistent with a primary marine boron signature as expected from the submarine-exhalative model for the gold prospects. We conclude from this that tourmaline formed or recrystallized from crustal fluids related to the amphibolite-grade metamorphism which affected the Serra do Itaberaba Group and that gold deposition occurred syn- to post-peak metamorphism by phase immiscibility, as attested by fluid inclusions in Tapera Grande tourmalinite tourmaline and quartz. The vein-hosted tourmalines at Quartzito have isotopically variable boron signatures, with heavier delta(11)B values of -5 parts per thousand to -8 parts per thousand for acicular green tourmalines and lighter values (-15 parts per thousand to -7 parts per thousand for light blue, Ti-firee tourmaline from quartz-carbonate veins). We attribute the heavier boron to fluids derived from the volcano-sedimentary rocks of marine affinity whereas the lighter boron was contributed by crustal fluids related to the granitoids or metasediments in the continental crust. (c) 2009 Elsevier B.V. All rights reserved.

Sr and Nd isotopic geochemistry of the early ultramafic-mafic rocks of the Mako bimodal volcanic belt of the Kedougou-Kenieba inlier (Senegal)

The Mako bimodal volcanic belt of the Kedougou-Kenieba inlier is composed of volcanic basalts and peridotites interbedded by quartzites and limestones intruded by different generations of granitoids. The early volcanic episode of the belt is constituted of submarine basalts with peridotite similar to those of the oceanic abyssal plains. It is intruded by the Badon Kakadian TTG-granitic batholite dated around 2200 Ma. The second volcanic phase is constituted of basaltic, andesitic, and felsitic flows exhibit structures of aerial volcanic rocks. It is intruded by granites dated between 2160 and 2070 Ma. The general pattern of trace element variation of submarine volcanic rocks is consistent with those of basalts from oceanic plateaus which are the modern equivalent of the Archean greenstones belts. The Nd and Sr isotopic systematics typical of juvenile material indicates that the source of these igneous rocks is derived from a depleted mantle source. These results are consistent with the idea of a major accretion within the West African Craton occurring at about 2.1 Ga and corresponding to an important process of mantle-oceanic lithosphere differentiation.