(Table T1) Coral taxa and their ecological significance in ODP Site 194-1196 and Hole 194-1199A sediments

The Southern Marion Plateau (SMP) represents a vertical stacking of Miocene carbonate platform deposits. Two sites (1196 and 1199) were drilled on top of this plateau, penetrating a 663-m carbonate succession of bioclastic and reefal sedimentary bodies. The study focuses on the least dolomitized 410-m-thick upper part of the succession, which is middle to late Miocene in age. Sedimentological and paleontological studies were conducted at both sites in order to propose a paleoenvironmental model and its evolution through the Miocene age. Six main microfacies of possible environmental significance were defined using statistical multivariate analyses, based on the recognition and point counting of 24 biogenic components. Depositional environment reconstructions are proposed as well as the biosedimentary and the environmental evolution regarding seismic architectures, stratigraphy, biosedimentology, and microfacies analysis. The SMP platform mainly results from a vertical stacking of lens-shaped bodies in homoclinal to distally steepened ramp settings.

Biostratigraphic significance of the calcareous nannofossil genus Reticulofenestra in the Upper Pliocene of the North Atlantic

We demonstrate size fluctuations of the calcareous nannofossil genus Reticulofenestra in Upper Pliocene sediments from the North Atlantic Ocean and clarify a characteristic evolutionary trend of this genus. Four bioevents, which are based on abrupt decreases in maximum size and on changes of morphologic features of Reticulofenestra specimens, are detected in the sediments. They are the disappearance of R. minutula var. A, the termination of Acme Zone II of R. minutula var. C, the disappearance of R. minutula var. B, and the termination of Acme Zone I of R. minutula var. C, in ascending order. These are nearly synchronous and traceable events.

The occurrence and significance of Pleistocene and Upper Pliocene sapropels

Numerous sapropels and sapropelic strata from Upper Pliocene and Pleistocene hemipelagic sediments of the Tyrrhenian Sea show that intermittent anoxia, possibly related to strongly increased biological productivity, was not restricted to the eastern Mediterranean basins and may be a basin-wide result of Late Pliocene-Pleistocene climatic variability. Even though the sapropel assemblage of the Tyrrhenian Sea clearly originates from multiple processes such as deposition under anoxic conditions or during spikes in surface water productivity and lateral transport of organic-rich suspensates, many "pelagic sapropels" have been recognized. Stratigraphic ages calculated for the organic-rich strata recovered during ODP Leg 107 indicate that the frequency of sapropel formation increased from the lowermost Pleistocene to the base of the Jaramillo magnetic event, coinciding with a period when stable isotope records of planktonic foraminifera indicate the onset of climatic cooling in the Mediterranean. A second, very pronounced peak in sapropel formation occurred in the Middle to Late Pleistocene (0.73-0.26 Ma). Formainifers studied in three high-resolution sample sets suggest that changes in surface-water temperature may have been responsible for establishing anoxic conditions, while salinity differences were not noted in the faunal assemblage. However, comparison of sapropel occurrence at Site 653 with the oxygen isotopic record of planktonic foraminifers established by Thunell et al. (1990, doi:10.2973/odp.proc.sr.107.155.1990) indicates that sapropel occurrences coincide with negative d18O excursions in planktonic foraminifers in thirteen of eighteen sapropels recognized in Hole 653A. A variant of the meltwater hypothesis accepted for sapropel formation in the Late Pleistocene eastern Mediterranean may thus be the cause of several "anoxic events" in the Tyrrhenian as well. Model calculations indicate that the amount of oxygen advection from Western Mediterranean Deep Water exerts the dominant control on the oxygen content in deep water of the Tyrrhenian Sea. Inhibition of deep-water formation in the northern Adriatic and the Balearic Basin by increased meltwater discharge and changing storm patterns during climatic amelioration may thus be responsible for sapropel formation in the Tyrrhenian Sea.

The Japan-Peru FTA : antecedents, significance and main features

The Economic Partnership Agreement (EPA) between Japan and Peru came into effect on March 1, 2012. This paper provides background information about this agreement's significance, mostly from a Peruvian point of view. It focuses on the following subjects: the statistical trends showing Peru's declining shares in Japan's trade and investment flows with Latin American countries between the mid-1970s and mid-2000s, the main explanatory factors of such a deterioration in Peru's economic position over that period, the changes of trade policy strategy in both countries since the 2000s, and the EPA negotiation process and some of its key results as featured in the text of the agreement.

New data on the specular reflectance of ores (VNIR: 400 - 1000 nm) and their significance for ore microscopy

This work is part of the project CAMEVA for the development of an expert system aimed at the automatic identification of ores [1, 2]. It relies on the measure of their reflectance values, R, on digital images. Software for calibration, acquisition and analysis of the multispectral data was designed by AITEMIN [3]; the research was also assessed by H.J. Bernhardt and E. Pirard [1].

Sensitisation to Act 2d in patientsallergic to Alternaria alternanta: an epiphenomenom without clinical significance?

In the last few years, the introduction of microarrays in the diagnosis of type I allergy is allowing the clinicians to have a much more accurate picture of their allergenic profile. However, the simultaneous measurement of specific IgE to multiple molecules can show unexpected sensitisations, without knowing their clinical relevance. For instance, we have been observing a high prevalence (74%) of sensitisation to Act d 2 (the thaumatin of kiwifruit) in patients sensitised to Alt a 1 (major allergen of Alternaria alternata) with a confirmed allergy to this mould. The aim of the present study was to clarify if there was any clinical relevance in this finding.

Significance of chaperonin 10-mediated inhibition of ATP hydrolysis by chaperonin 60

Chaperonins are essential for the folding of proteins in bacteria, mitochondria, and chloroplasts. We have functionally characterized the yeast mitochondrial chaperonins hsp60 and hsp10. In the presence of ADP, one molecule of hsp10 binds to hsp60 with an apparent Kd of 0.9 nM and a second molecule of hsp10 binds with a Kd of 24 nM. In the presence of ATP, the purified yeast chaperonins mediate the refolding of mitochondrial malate dehydrogenase. Hsp10 inhibits the ATPase activity of hsp60 by about 40%. Hsp10(P36H) is a point mutant of hsp10 that confers temperature-sensitive growth to yeast. Consistent with the in vivo phenotype, refolding of mitochondrial malate dehydrogenase in the presence of purified hsp10(P36H) and hsp60 is reduced at 25°C and abolished at 30°C. The affinity of hsp10(P36H) to hsp60 as well as to Escherichia coli GroEL is reduced. However, this decrease in affinity does not correlate with the functional defect, because hsp10(P36H) fully assists the GroEL-mediated refolding of malate dehydrogenase at 30°C. Refolding activity, rather, correlates with the ability of hsp10(P36H) to inhibit the ATPase of GroEL but not that of hsp60. Based on our findings, we propose that the inhibition of ATP hydrolysis is mechanistically coupled to chaperonin-mediated protein folding.

Measurement of community metabolism and significance in the coral reef CO2 source-sink debate

Two methods are commonly used to measure the community metabolism (primary production, respiration, and calcification) of shallow-water marine communities and infer air–sea CO2 fluxes: the pH-total alkalinity and pH-O2 techniques. The underlying assumptions of each technique are examined to assess the recent claim that the most widely used technique in coral reefs (pH-total alkalinity), may have provided spurious results in the past because of high rates of nitrification and release of phosphoric acid in the water column [Chisholm, J. R. M. & Barnes, D. J. (1998) Proc. Natl. Acad. Sci. USA 95, 6566–6569]. At least three lines of evidence suggest that this claim is not founded. First, the rate of nitrification required to explain the discrepancy between the two methods recently reported is not realistic as it is much higher than the rates measured in another reef system and greater than the highest rate measured in a marine environment. Second, fluxes of ammonium, nitrate, and phosphorus are not consistent with high rates of nitrification and release of phosphoric acid. Third, the consistency of the metabolic parameters obtained by using the two techniques is in good agreement in two sites recently investigated. The pH-total alkalinity technique therefore appears to be applicable in most coral reef systems. Consequently, the conclusion that most coral reef flats are sources of CO2 to the atmosphere does not need revision. Furthermore, we provide geochemical evidence that calcification in coral reefs, as well as in other calcifying ecosystems, is a long-term source of CO2 for the atmosphere.

Specific intercellular binding of the β-amyloid precursor protein to the presenilins induces intercellular signaling: Its significance for Alzheimer’s disease

Genetic evidence has implicated three proteins, the β-amyloid precursor protein (β-APP) and the two homologous presenilins (PS-1 and PS-2), in the etiology of Alzheimer’s disease (AD). How these three proteins jointly contribute to AD, however, is not clear. Nor is any of their normal physiological functions known. Herein, we demonstrate, confirming a prediction made earlier, that β-APP and either PS-1 or PS-2 act as a specific membrane-bound ligand binding intercellularly with either of its two membrane receptors. This results in a cell–cell adhesion, after which rapid transient increases in protein tyrosine kinase activity and protein tyrosine phosphorylation occur coordinately inside one or both of the two adherent cells. The spectrum of proteins modified by tyrosine phosphorylation differs depending on whether PS-1 or PS-2 is involved in the specific intercellular binding to β-APP, which implies that PS-1 and PS-2 have distinct, rather than redundant, functions in normal physiology. The relevance of this intercellular interaction and signaling process to AD is discussed.

Synthesis, Storage, and Release of Vascular Endothelial Growth Factor/Vascular Permeability Factor (VEGF/VPF) by Human Mast Cells: Implications for the Biological Significance of VEGF206

Mast cells have been implicated in various diseases that are accompanied by neovascularization. The exact mechanisms by which mast cells might mediate an angiogenic response, however, are unclear and therefore, we have investigated the possible expression of vascular endothelial growth factor/vascular permeability factor (VEGF/VPF) in the human mast cell line HMC-1 and in human skin mast cells. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that mast cells constitutively express VEGF121, VEGF165, and VEGF189. After a prolonged stimulation of cells for 24 h with phorbol 12-myristate 13-acetate (PMA) and the ionophore A23187, an additional transcript representing VEGF206 was detectable, as could be verified by sequence analysis. These results were confirmed at the protein level by Western blot analysis. When the amounts of VEGF released under unstimulated and stimulated conditions were compared, a significant increase was detectable after stimulation of cells. Human microvascular endothelial cells (HMVEC) responded to the supernatant of unstimulated HMC-1 cells with a dose-dependent mitogenic effect, neutralizable up to 90% in the presence of a VEGF-specific monoclonal antibody. Flow cytometry and postembedding immunoelectron microscopy were used to detect VEGF in its cell-associated form. VEGF was exclusively detectable in the secretory granules of isolated human skin mast cells. These results show that both normal and leukemic human mast cells constitutively express bioactive VEGF. Furthermore, this study contributes to the understanding of the physiological role of the strongly heparin-binding VEGF isoforms, since these were found for the first time to be expressed in an activation-dependent manner in HMC-1 cells.

Statistical significance of protein structure prediction by threading

In this study, we estimate the statistical significance of structure prediction by threading. We introduce a single parameter ɛ that serves as a universal measure determining the probability that the best alignment is indeed a native-like analog. Parameter ɛ takes into account both length and composition of the query sequence and the number of decoys in threading simulation. It can be computed directly from the query sequence and potential of interactions, eliminating the need for sequence reshuffling and realignment. Although our theoretical analysis is general, here we compare its predictions with the results of gapless threading. Finally we estimate the number of decoys from which the native structure can be found by existing potentials of interactions. We discuss how this analysis can be extended to determine the optimal gap penalties for any sequence-structure alignment (threading) method, thus optimizing it to maximum possible performance.