Marine isocyanides and related natural products structure, biosynthesis and ecology

This review highlights structural and biosynthetic work on a group of nitrogen-functionalised terpenes that are almost exclusively found in marine invertebrates and the animals that feed on them. The chemical functionality reviewed includes isocyanides, isothiocyanates, formamides, thiocyanates, isocyanates, and dichloroimines. The literature through mid 2003 is reviewed and there are 143 citations.

Shoemaker impact structure, Western Australia

The Shoemaker impact structure, on the southern margin of the Palaeoproterozoic Earaheedy Basin, with an outer diameter of similar to30 km, consists of two well-defined concentric ring structures surrounding a granitoid basement uplift. The concentric structures, including a ring syncline and a ring anticline, formed in sedimentary rocks of the Earaheedy Group. In addition, aeromagnetic and geological field observations suggest that Shoemaker is a deeply eroded structure. The central 12 km-diameter uplift consists of fractured Archaean basement granitoids of syenitic composition (Teague Granite). Shock-metamorphic features include shatter cones in sedimentary rocks and planar deformation features in quartz crystals of the Teague Granite. Universal-stage analysis of 51 sets of planar deformation features in 18 quartz grains indicate dominance of sets parallel to omega (10 (1) over bar3}, but absence of sets parallel to pi (10 (1) over bar2}, implying peak shock pressures in the range of 10-20 GPa for the analysed sample. Geophysical characteristics of the structure include a -100 mus(-2) gravity anomaly coincident with the central uplift and positive circular trends in both magnetic and gravity correlating with the inner ring syncline and outer ring anticline. The Teague Granite is dominated by albite-quartz-K-feldspar with subordinate amounts of alkali pyroxene. The alkali-rich syenitic composition suggests it could either represent a member of the Late Archaean plutonic suite or the product of alkali metasomatism related to impact-generated hydrothermal activity. In places, the Teague Granite exhibits partial to pervasive silicification and contains hydrothermal minerals, including amphibole, garnet, sericite and prehnite. Recent isotopic age studies of the Teague Granite suggest an older age limit of ca 1300 Ma (Ar-Ar on K-feldspar) and a younger age limit of ca 568 Ma (K-Ar on illite-smectite). The significance of the K-Ar age of 568 Ma is not clear, and it might represent either hydrothermal activity triggered by impact-related energy or a possible resetting by tectonothermal events in the region.

The Quaternary pyroclastic succession of southeast Tenerife, Canary Islands: Explosive eruptions, related caldera subsidence, and sector collapse

A much-revised Quaternary stratigraphy is presented for ignimbrites and pumice fall deposits of the Bandas del Sur, in southern Tenerife. New Ar-41/Ar-39 data obtained for the Arico, Granadilla, Fasnia, Poris, La Caleta and Abrigo formations are presented, allowing correlation with previously dated offshore marine ashfall layers and volcaniclastic sediments. We also provide a minimum age of 287 +/- 7 ka for a major sector collapse event at the Gaimar valley. The Bandas del Sur succession includes more than seven widespread ignimbrite sheets that have similar characteristics, including widespread basal Plinian layers, predominantly phonolite composition, ignimbrites with similar extensive geographic distributions, thin condensed veneers with abundant diffuse bedding and complex lateral and vertical grading patterns, lateral gradations into localized massive facies within palaeo-wadis, and widespread lithic breccia layers that probably record caldera-forming eruptions. Each ignimbrite sheet records substantial bypassing of pyroclastic material into the ocean. The succession indicates that Las Canadas volcano underwent a series of major explosive eruptions, each starting with a Plinian phase followed by emplacement of ignimbrites and thin ash layers, some of coignimbrite origin. Several of the ignimbrite sheets are compositionally zoned and contain subordinate mafic pumices and banded pumices indicative of magma mingling immediately prior to eruption. Because passage of each pyroclastic density current was characterized by phases of non-deposition and erosion, the entire course of each eruption is incompletely recorded at any one location, accounting for some previously perceived differences between the units. Because each current passed into the ocean, estimating eruption volumes is virtually impossible. Nevertheless, the consistent widespread distributions and the presence of lithic breccias within most of the ignimbrite sheets suggest that at least seven caldera collapse eruptions are recorded in the Bandas del Sur succession and probably formed a complex, nested collapse structure. Detailed field relationships show that extensive ignimbrite sheets (e.g. the Arico, Poris and La Caleta formations) relate to previously unrecognized caldera collapse events. We envisage that the evolution of the nested Las Cahadas caldera is more complex than previously thought and involved a protracted history of successive ignimbrite-related caldera collapse events, and large sector collapse events, interspersed with edifice-building phases.

Structure and metal binding studies of the second copper binding domain of the Menkes ATPase

Biological utilisation of copper requires that the metal, in its ionic forms, be meticulously transported, inserted into enzymes and regulatory proteins, and excess be excreted. To understand the trafficking process, it is crucial that the structures of the proteins involved in the varied processes be resolved. To investigate copper binding to a family of structurally related copper-binding proteins, we have characterised the second Menkes N-terminal domain (MNKr2). The structure, determined using H-1 and N-15 heteronuclear NMR, of the reduced form of MNKr2 has revealed two alpha-helices lying over a single beta-sheet and shows that the binding site, a Cys(X)(2)Cys pair, is located on an exposed loop. H-1-N-15 HSQC experiments demonstrate that binding of Cu(I) causes changes that are localised to conserved residues adjacent to the metal binding site. Residues in this area are important to the delivery of copper by the structurally related Cu(I) chaperones. Complementary site-directed mutagenesis of the adjacent residues has been used to probe the structural roles of conserved residues. (C) 2003 Published by Elsevier Inc.

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or 'twin' formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.

The 3-D Structure of Polycrystalline Diamond Film by Electron Backscattering Diffraction (EBSD)

A lithographic method was used to produce polycrystalline diamond films having highly defined surface geometry, showing an array of diamond tips for possible application as a field emitter device. The films grown in this study used microwave plasma assisted chemical vapour deposition (MACVD) on a silicon substrate; the substrate was then dissolved away to reveal the surface features on the diamond film. It is possible to align the crystallite direction and affect the electron emission properties using a voltage bias to enhance the nucleation process and influence the nuclei to a preferred orientation. This study focuses on the identification of the distribution of crystal directions in the film, using electron backscattering diffraction (EBSD) to identify the crystallographic character of the film surface. EBSD allows direct examination of the individual diamond grains, grains boundaries and the crystal orientation of each individual crystallite. The EBSD maps of the bottom (nucleation side) of the films, following which a layer of film is ion-milled away and the mapping process repeated. The method demonstrates experimentally that oriented nucleation occurs and the thin sections allow the crystal texture to be reconstructed in 3-D. (C) 2003 Elsevier B.V. All rights reserved.

Psychometric properties of the drinking expectancy questionnaire: A review of the factor structure and a proposed new scoring method

Objective: Expectancies about the outcomes of alcohol consumption are widely accepted as important determinants of drinking. This construct is increasingly recognized as a significant element of psychological interventions for alcohol-related problems. Much effort has been invested in producing reliable and valid instruments to measure this construct for research and clinical purposes, but very few have had their factor structure subjected to adequate validation. Among them, the Drinking Expectancies Questionnaire (DEQ) was developed to address some theoretical and design issues with earlier expectancy scales. Exploratory factor analyses, in addition to validity and reliability analyses, were performed when the original questionnaire was developed. The object of this study was to undertake a confirmatory analysis of the factor structure of the DEQ. Method: Confirmatory factor analysis through LISREL 8 was performed using a randomly split sample of 679 drinkers. Results: Results suggested that a new 5-factor model, which differs slightly from the original 6-factor version, was a more robust measure of expectancies. A new method of scoring the DEQ consistent with this factor structure is presented. Conclusions: The present study shows more robust psychometric properties of the DEQ using the new factor structure.

West nile virus core protein: Tetramer structure and ribbon formation

We have determined the crystal structure of the core (C) protein from the Kunjin subtype of West Nile virus (WNV), closely related to the NY99 strain of WNV, currently a major health threat in the U.S. WNV is a member of the Flaviviridae family of enveloped RNA viruses that contains many important human pathogens. The C protein is associated with the RNA genome and forms the internal core which is surrounded by the envelope in the virion. The C protein structure contains four a. helices and forms dimers that are organized into tetramers. The tetramers form extended filamentous ribbons resembling the stacked alpha helices seen in HEAT protein structures.

Clustering of related individuals in a population of the Australian lizard, Egernia frerei

Stable social aggregations are rarely recorded in lizards, but have now been reported from several species in the Australian scincid genus Egernia. Most of those examples come from species using rock crevice refuges that are relatively easy to observe. But for many other Egernia species that occupy different habitats and are more secretive, it is hard to gather the observational data needed to deduce their social structure. Therefore, we used genotypes at six polymorphic microsatellite DNA loci of 229 individuals of Egernia frerei, trapped in 22 sampling sites over 3500 ha of eucalypt forest on Fraser Island, Australia. Each sampling site contained 15 trap locations in a 100 x 50 m grid. We estimated relatedness among pairs of individuals and found that relatedness was higher within than between sites. Relatedness of females within sites was higher than relatedness of males, and was higher than relatedness between males and females. Within sites we found that juvenile lizards were highly related to other juveniles and to adults trapped at the same location, or at adjacent locations, but relatedness decreased with increasing trap separation. We interpreted the results as suggesting high natal philopatry among juvenile lizards and adult females. This result is consistent with stable family group structure previously reported in rock dwelling Egernia species, and suggests that social behaviour in this genus is not habitat driven.

Probing the pore wall structure of nanoporous carbons using adsorption

Hitherto, adsorption has been traditionally used to study only the porous structure in disordered materials, while the structure of the solid phase skeleton has been probed by crystallographic methods such as X-ray diffraction. Here we show that for carbons density functional theory, suitably adapted to consider heterogeneity of the pore walls, can be reliably used to probe features of the solid structure hitherto accessibly only approximately even by crystallographic methods. We investigate a range of carbons and determine pore wall thickness distributions using argon adsorption, with results corroborated by X-ray diffraction.

Magnetosomal matrix: ultrafine structure may template biomineralization of magnetosomes

The organic matrix surrounding bullet-shaped, cubo-octahedral, D-shaped, irregular arrowhead-shaped, and truncated hexa-octahedral magnetosomes was analysed in a variety of uncultured magnetotactic bacteria. The matrix was examined using low- (80 kV) and intermediate- (400 kV) voltage TEM. It encapsulated magnetosomes in dehydrated cells, ultraviolet-B-irradiated dehydrated cells and stained resin-embedded fixed cells, so the apparent structure of the matrix does not appear to be an artefact of specimen preparation. High-resolution images revealed lattice fringes in the matrix surrounding magnetite and greigite magnetosomes that were aligned with lattice fringes in the encapsulated magnetosomes. In all except one case, the lattice fringes had widths equal to or twice the width of the corresponding lattice fringes in the magnetosomes. The lattice fringes in the matrix were aligned with the {311}, {220}, {331}, {111} and {391} related lattice planes of magnetite and the {222} lattice plane of greigite. An unidentified material, possibly an iron hydroxide, was detected in two immature magnetosomes containing magnetite. The unidentified phase had a structure similar to that of the matrix as it contained {311}, {220} and {111} lattice fringes, which indicates that the matrix acts as a template for the spatially controlled biomineralization of the unidentified phase, which itself transforms into magnetite. The unidentified phase was thus called pre-magnetite. The presence of the magnetosomal matrix explains all of the five properties of the biosignature of the magnetosomal chain proposed previously by Friedmann et al. and supports their claim that some of the magnetite particles in the carbonate globules in the Martian meteorite ALH84001 are biogenic. Two new morphologies of magnetite magnetosomes are also reported here (i.e. tooth-shaped and hexa-octahedral magnetosomes). Tooth-shaped magnetite magnetosomes elongated in the [110] direction are reported, and are distinct from arrowhead-shaped and bullet-shaped magnetosomes. Elongation of magnetite magnetosomes in the [110] direction has not been reported previously. A Martian hexa-octahedral magnetite particle was previously characterized by Thomas-Keptra et al. and compared with truncated hexa-octahedral magnetite magnetosomes. Hexa-octahedral magnetite magnetosomes with the same morphology and similar sizes and axial ratios as those reported by Thomas-Keptra et al. are characterized here. These observations support their claim that ALH84001 contains evidence for a past Martian biota.