Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Palaeoclimatic implications of the growth history and stable isotope (delta O-18 and delta C-13) geochemistry of a Middle to Late Pleistocene stalagmite from central-western Italy

The age structure and, stable isotope composition of a stalagmite (CC I) from an upland cave in central-western Italy were studied to investigate regional response to global climatic changes. Four growth phases are constrained by 28 thermal ionization and multi-collector inductively coupled plasma mass spectrometry Th-U ages and reveal intermittent deposition through the period between Marine isotope Stage (MIS) 11 and 3 (similar to380 and similar to43 kyr). Most of the growth took place between similar to380 and similar to280 kyr, a period punctuated briefly by a hiatus in deposition through the glacial maximum of MIS 10. Growth was terminated abruptly at 280 kyr just prior to the MIS 8 glacial maximum. With a present-day chamber temperature of 7.5 degreesC, the timing of hiatuses close to these glacial maxima point to freezing conditions at the time. No deposition was recorded through the entirety of MIS 7 and most of MIS 6, whilst two minor growth phases occurred at similar to141-125 and similar to43 kyr. Growth at 141 kyr indicates temperatures >0 degreesC at a time when MIS 6 ice volumes were close to their maximum. High stable carbon isotope (delta(13)C) values (similar to2.8parts per thousand to +3.1parts per thousand) throughout the stalagmite's growth reflect a persistently low input of biogenic CO2, indicating that the steep, barren and alpine-like recharge area of today ha's been in existence for at least the last similar to380 kyr. During MIS 9, the lowest delta(13)C values occur well after maximum interglacial conditions, suggesting a lag in the development of post-glacial soils in this high-altitude karst. The stable oxygen isotope (delta(18)O) trends match the main structural features of the major climate proxy records (SPECMAP, Vostok and Devils Hole), suggesting that the delta(18)O of CC1 has responded to global-scale climate changes, whilst remarkable similarity exists between CC1 delta(18)O and regional sea-surface temperature reconstructions from North Atlantic core ODP980 and southwest Pacific marine core MD97-2120 through the most detailed part of the CC1 record, MIS 9-8. The results suggest that CC1 and other stalagmites from the cave have the potential to capture a long record of regional temperature trends, particularly in regards to the relative severity of Pleistocene glacial stages. (C) 2004 Elsevier B.V. All rights reserved.

Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 angstrom) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

High-precision TIMS U-series and AMS C-14 dating of a coral reef lagoon sediment core from southern South China Sea

Accurate dating of lagoon sediments has been a difficult problem, although lagoon profiles, usually with high deposition rates, have a great potential for high-resolution climate reconstruction. We report 26 high-precision TIMS U-series dates (on 25 coral branches) and five AMS C-14 dates (on foraminifera) for a 15.4-m long lagoon core from Yongshu Reef, Nansha area, southern South China Sea. All the dates are in the correct stratigraphical sequence, providing the best chronology so far reported for lagoon deposits. The results reveal a similar to 4000-a continuous depositional history, with sedimentation rates varying from 0.8 to 24.6 mm a(-1), with an average of 3.85 mm a(-1), which corresponds to an average net carbonate accumulation rate of similar to 2700 g CaCO3 m(-2) a(-1), significantly higher than the mean value (800 +/- 400 g CaCO3 m(-2) a(-1)) used for lagoons in general in previous studies of global carbonate budget. Episodes of accelerated depositions within the last 1000 years correlate well with strong storm events identified by U-series dates of storm-transported coral blocks in the area. However, in the longer term, the sedimentation rates during the past 1000 years were much higher than earlier on, probably due to more vigorous wave-reef interaction as a result of relative sea-level fall since 500 AD and expansion of reef flat area, supplying more sediments. The coral TIMS U-series ages and foraminifera AMS 14C dates reveal intriguing apparent radiocarbon reservoir ages (R) from 572 to 1052 years, which are much higher than global mean values of similar to 400 years. (c) 2006 Elsevier Ltd. All rights reserved.

Structural, electrical, and optical analysis of ion implanted semi-insulating InP

Semi-insulating InP was implanted with MeV P, As, Ga, and In ions, and the resulting evolution of structural properties with increased annealing temperature was analyzed using double crystal x-ray diffractometry and cross sectional transmission electron microscopy. The types of damage identified are correlated with scanning spreading resistance and scanning capacitance measurements, as well as with previously measured Hall effect and time resolved photoluminescence results. We have identified multiple layers of conductivity in the samples which occur due to the nonuniform damage profile of a single implant. Our structural studies have shown that the amount and type of damage caused by implantation does not scale with implant ion atomic mass. (C) 2004 American Institute of Physics.

Adiponectin and its receptors in patients with chronic hepatitis C

Background/Aims: There is increasing interest in the influence of excess body weight and associated metabolic factors on the liver. In patients with non-alcoholic steatohepatitis, lower levels of adiponectin were associated with higher grades of hepatic steatosis and necroinflammatory activity, suggesting a pathophysiological role for this adipokine in liver disease. Methods: We studied 194 consecutive patients with untreated chronic HCV, to assess the relationship between adiponectin and its receptors and hepatic steatosis, fibrosis and inflammation. Results: Significant negative correlations between serum adiponectin and male gender, body mass index and serum insulin were observed. However, there was no association between serum adiponectin and stage of fibrosis and lower levels of serum adiponectin were associated with the presence of steatosis in males only. In contrast, there was a significant increase in serum adiponectin and hepatic adiponectin immunoreactivity with increasing inflammation. The hepatic mRNA expression of the adiponectin receptors, AdipoR1 and AdipoR2, displayed significant but opposite associations with phosphoenolpyruvate carboxykinase (PEPCK) gene expression, a substitute marker of hepatic insulin sensitivity. Conclusions: In patients with chronic HCV, adiponectin was associated with steatosis only in males and was paradoxically increased with inflammation. Our results suggest that the role of adiponectin in chronic liver diseases may be linked to gender and etiology. (c) 2005 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Explaining point variability in the eastern Victoria river region, northern territory

This paper constructs a reduction sequence model for north Australian points from the eastern Victoria River region, and identifies a single continuum linking unifacial and bifacial point forms, with some divergence from this single reduction trajectory dependent upon artefact size. Chronological changes in reduction intensity between 5,000BP and the present are found to coincide with typological variation in points as well as changing emphasis on the extendibility of point reduction. It is suggested that changes in the extendibility of point reduction can be linked to intensified ENSO-driven climatic variability in the late Holocene that likely increased economic risk and warranted a substantial technological response, including the use of retouched toolkits with potential for longer use-lives.