Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The gaseous environment of radio galaxies: a new perspective from high-resolution x-ray spectroscopy

It is known that massive black holes have a profound effect on the evolution of galaxies, and possibly on their formation by regulating the amount of gas available for the star formation. However, how black hole and galaxies communicate is still an open problem, depending on how much of the energy released interacts with the circumnuclear matter. In the last years, most studies of feedback have primarily focused on AGN jet/cavity systems in the most massive galaxy clusters. This thesis intends to investigate the feedback phenomena in radio--loud AGNs from a different perspective studying isolated radio galaxies, through high-resolution spectroscopy. In particular one NLRG and three BLRG are studied, searching for warm gas, both in emission and absorption, in the soft X-ray band. I show that the soft spectrum of 3C33 originates from gas photoionized by the central engine. I found for the first time WA in 3C382 and 3C390.3. I show that the observed warm emitter/absorbers is not uniform and probably located in the NLR. The detected WA is slow implying a mass outflow rate and kinetic luminosity always well below 1% the L(acc) as well as the P(jet). Finally the radio--loud properties are compared with those of type 1 RQ AGNs. A positive correlation is found between the mass outflow rate/kinetic luminosity, and the radio loudness. This seems to suggest that the presence of a radio source (the jet?) affects the distribution of the absorbing gas. Alternatively, if the gas distribution is similar in Seyferts and radio galaxies, the M(out) vs rl relation could simply indicate a major ejection of matter in the form of wind in powerful radio AGNs.

Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

High-resolution imaging of 2D outer membrane protein F (OmpF) crystals by atomic force microscopy

In this chapter the methodological bases are provided to achieve subnanometer resolution on two-dimensional (2D) membrane protein crystals by atomic force microscopy (AFM). This is outlined in detail with the example of AFM studies of the outer membrane protein F (OmpF) from the bacterium Escherichia coli (E. coli). We describe in detail the high-resolution imaging of 2D OmpF crystals in aqueous solution and under near-physiological conditions. The topographs of OmpF, and stylus effects and artifacts encountered when imaging by AFM are discussed.

High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes.

Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.

Petrology and geochemistry of basalts from the Vavilov Basin

During ODP Leg 107, two holes were drilled in the basement of Vavilov Basin, a central oceanic area of the Tyrrhenian sea. Hole 655B is located near the Gortani ridge in off-axis position at the western rim of the basin; Hole 651A is located on a basement swell at the axis of the basin. This paper deals with mineral chemistry, major and trace element geochemistry, and petrogenesis of the basalts recovered in the two holes. The mineralogy of the basalts is broadly homogeneous, but all of them have suffered important seawater alteration. Their major-element compositions are similar to both normal-mid-ocean-ridge-basalts (N-MORB) and back-arc-basalts (BAB) except for Na2O contents (BAB-like), and K2O which is somewhat enriched in upper unit of Hole 651 A. Their affinity with N-MORB and BAB is confirmed by using immobile trace elements such as Zr, Y, and Nb. However, basalts from the two sites present contrasting geochemical characteristics on spidergrams using incompatible elements. Hole 655B basalts are homogeneous enriched tholeiites, similar to those from DSDP Hole 373 (located on the opposite side of the basin near the eastern rim), and show affinities with enriched MORB (E-MORB). At Hole 651 A, the two basalt units are chemically distinct. One sample recovered in lower unit is rather similar to those from Hole 655B, but basalts from upper unit display calc-alkaline characteristic evidenced by the increase of light-ion-lithophile-element (LILE)/high-field-strength-element (HFSE) ratio, and appearance of a negative Nb-anomaly, making them comparable with orogenic lavas from the adjacent Eolian arc. The observed chemical compositions of the basalts are consistent with a derivation of the magmas from a N-MORB type source progressively contaminated by LILE-enriched fluids released from dehydration of the bordering subducted plate. Implications for evolution of the Tyrrhenian basin are tentatively proposed taking into consideration geochemical and chronological relationships between basalts from Leg 107 Holes 655B and 651 A, together with data from Leg 42 Site 373 and Vavilov Seamount. These data illustrate back-arc spreading in ensialic basin closely associated with the maturation of the adjacent subduction, followed by the growth of late off-axis central volcano, whereas the active subduction retreats southeastward.

Petrography and geochemistry of basement rocks from five DSDP Leg 60 Sites

Bulk chemistry and trace elements data were measured in 72 samples, selected from 5 basement sections, which have been recovered by Leg 60 drilling (Sites 453, 454, 456, 458, and 459). According to analytical results a metagabbro- metabasalt breccia, deposited about 5 Ma at the westernmost flank of the Mariana Trough (Site 453), was derived from an island arc source. Basalts from the Mariana Trough (Sites 454 and 456) are similar in many respects to midoceanic ridge basalts (MORB). Yet rocks of unusual geochemistry, reflecting the possible influence of arc volcanism, were found among the pillow lavas at the easternmost trough (Site 456). The acoustic basement in the Mariana fore-arc region was formed by submarine eruptions of arc tholeiites (Sites 458 and 459) and peculiar high-MgO andesites related to the boninite suite.

High resolution paleoceanography of the Guaymas Basin, Gulf of California, during the past 15000 yeras

Deep Sea Drilling Project Site 480 (27°54.10'N, 111°39.34'W; 655 m water depth) contains a high resolution record of paleoceanographic change of the past 15000 years for the Guaymas Basin, a region of very high diatom productivity within the central Gulf of California. Analyses of diatoms and silicoflagellates were completed on samples spaced every 40-50 yr, whereas ICP-AES geochemical analyses were completed on alternate samples (sample spacing 80-100 yr). The Bolling-Allerod interval (14.6-12.9 ka) (note, ka refers to 1000 calendar years BP throughout this report) is characterized by an increase in biogenic silica and a decline in calcium carbonate relative to surrounding intervals, suggesting conditions somewhat similar to those of today. The Younger Dryas event (12.9-11.6 ka) is marked by a major drop in biogenic silica and an increase in calcium carbonate. Increasing relative percentage contributions of Azpeitia nodulifera and Dictyocha perlaevis (a tropical diatom and silicoflagellate, respectively) and reduced numbers of the silicoflagellate Octactis pulchra are supportive of reduced upwelling of nutrient-rich waters. Between 10.6 and 10.0 ka, calcium carbonate and A. nodulifera abruptly decline at DSDP 480, while Roperia tesselata, a diatom indicative of winter upwelling in the modern-day Gulf, increases sharply in numbers. A nearly coincident increase in the silicoflagellate Dictyocha stapedia suggests that waters above DSDP 480 were more similar to the cooler and slightly more saline waters of the northern Gulf during much of the early and middle parts of the Holocene (~10 to 3.2 ka). At about 6.2 ka a stepwise increase in biogenic silica and the reappearance of the tropical diatom A. nodulifera marks a major change in oceanographic conditions in the Gulf. A winter shift to more northwesterly winds may have occurred at this time along with the onset of periodic northward excursions (El Nino-driven?) of the North Equatorial Countercurrent during the summer. Beginning between 2.8 and 2.4 ka, the amplitude of biogenic silica and wt% Fe, Al, and Ti (proxies of terrigenous input) increase, possibly reflecting intensification of ENSO cycles and the establishment of modern oceanographic conditions in the Gulf. Increased numbers of O. pulchra after 2.8 ka suggest enhanced spring upwelling.

Geochemistry of pelagic and hemipelagic sediments of ODP Leg 126 sites

Chemical analyses were performed on major, minor, and rare-earth elements of pelagic and hemipelagic sediments of the forearc, arc, and backarc sites of the Izu-Bonin Arc, Ocean Drilling Program Leg 126. Analyses of the hemipelagic and pelagic sediments of this area indicate that the chemical composition of this arc is highly affected by the chemical composition of rocks of this arc as a source of sediments. The Oligocene sediments, which are characterized by high MgO contents, reflect the chemical composition of the Paleogene volcanic rocks of the immature arc. Moreover, the late Miocene to Quaternary sediments with low MgO contents are attributed to the composition of the present arc. We also suggest that the sedimentation rates and topography of the sedimentary basin affect the MnO and SiO2 contents of pelagic and hemipelagic sediments.

Natural remanent magnetization (NRM) from ODP Site 1263 covering magnetochron C20r and C21n and high-resolution bulk carbon isotope (d13C) records from Sites 702 and 1263

To explore cause and consequences of past climate change, very accurate age models such as those provided by the astronomical timescale (ATS) are needed. Beyond 40 million years the accuracy of the ATS critically depends on the correctness of orbital models and radioisotopic dating techniques. Discrepancies in the age dating of sedimentary successions and the lack of suitable records spanning the middle Eocene have prevented development of a continuous astronomically calibrated geological timescale for the entire Cenozoic Era. We now solve this problem by constructing an independent astrochronological stratigraphy based on Earth's stable 405 kyr eccentricity cycle between 41 and 48 million years ago (Ma) with new data from deep-sea sedimentary sequences in the South Atlantic Ocean. This new link completes the Paleogene astronomical timescale and confirms the intercalibration of radioisotopic and astronomical dating methods back through the Paleocene-Eocene Thermal Maximum (PETM, 55.930 Ma) and the Cretaceous-Paleogene boundary (66.022 Ma). Coupling of the Paleogene 405 kyr cyclostratigraphic frameworks across the middle Eocene further paves the way for extending the ATS into the Mesozoic.

High resolution benthic stable-isotope records from ODP Site 1263 and 1262

Recent studies have shown that the Early Eocene Climatic Optimum (EECO) was preceded by a series of short-lived global warming events, known as hyperthermals. Here we present high-resolution benthic stable carbon and oxygen isotope records from ODP Sites 1262 and 1263 (Walvis Ridge, SE Atlantic) between ~54 and ~52 million years ago, tightly constraining the character, timing, and magnitude of six prominent hyperthermal events. These events, which include Eocene Thermal Maximum (ETM) 2 and 3, are studied in relation to orbital forcing and long-term trends. Our findings reveal an almost linear relationship between d13C and d18O for all these hyperthermals, indicating that the eccentricity-paced co-variance between deep-sea temperature changes and extreme perturbations in the exogenic carbon pool persisted during these events towards the onset of the EECO, in accord with previous observations for the Paleocene Eocene Thermal Maximum (PETM) and ETM2. The covariance of d13C and d18O during H2 and I2, which are the second pulses of the "paired" hyperthermal events ETM2-H2 and I1-I2, deviates with respect to the other events. We hypothesize that this could relate to a relatively higher contribution of an isotopically heavier source of carbon, such as peat or permafrost, and/or to climate feedbacks/local changes in circulation. Finally, the d18O records of the two sites show a systematic offset with on average 0.2 per mil heavier values for the shallower Site 1263, which we link to a slightly heavier isotopic composition of the intermediate water mass reaching the northeastern flank of the Walvis Ridge compared to that of the deeper northwestern water mass at Site 1262.