Total organic carbon, delta13C, biomarker, gas compilations and hopanoids analysis from IODP Sites 307-U1317 and 307-U1318

During the Integrated Ocean Drilling Program (IODP) Expedition 307 for the first time a cold-water coral carbonate mound was drilled down through its base into the underlying sediments. In the current study, sample material from within and below Challenger Mound, located in the Belgica carbonate mound province in the Porcupine Basin offshore Ireland, was investigated for its distribution of microbial communities and gas composition using biogeochemical and geochemical approaches to elucidate the question on the initiation of carbonate mounds. Past and living microbial populations are lower in the mound section compared to the underlying sediments or sediments of an upslope reference site. A reason for this might be a reduced substrate feedstock, reflected by low total organic carbon (TOC) contents, in the once coral dominated mound sequence. In contrast, in the reference site a lithostratigraphic sequence with comparatively high TOC contents shows higher abundances of both past and present microbial communities, indicating favourable living conditions from time of sedimentation until today. Composition and isotopic values of gases below the mound base seem to point to a mixed gas of biogenic and thermogenic origin with a higher proportion of biogenic gas. Oil-derived hydrocarbons were not detected at the mound site. This suggests that at least in the investigated part of the mound base the upward flow of fossil hydrocarbons, being one hypothesis for the initiation of the formation of carbonate mounds, seems to be only of minor significance.

Total organic carbon, bitumen ratio, hopane and sterane parameters of ODP Sites 128-798 and 128-799

Notable compositional changes of organic matter are observed below the silica transition zone in thermally immature sediments. The increase of bitumen ratio, and hopane and sterane isomerization parameters indicate an acceleration of the kinetics of the chemical reactions which transform the organic matter. This phenomenon is probably due to the numerous mineral and textural changes induced by the transformation of amorphous biogenic silica into crystalline authigenic silica.

Parabolae Salomonis ad veritatem hebraicam castigatae, & per ... Thomam de Vio Caietanum ... enarratae ... ; his accessere luculentissima eiusdem auctoris In Ecclesiasten & tria Isaiae capita commentaria, cum indice amplissimo.

Tractatus ... Thomae de Vio Caietani ... De coniungis regis Angliae cum relicta fratris sui (últimas [16] p.)

Lyra apostolica.

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Hermogenis Tarsensis rhetoris acutissimi De ratione inueniendi oratoria, libri IIII. /

Vol. 1 includes index at end.

Aristotelis Stagiritae Opera ... /

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Morphological variability of Globorotalia menardii in DSDP Sites 68-502 and 68-503

Variability in the test of Globorotalia menardii during the past 8 million years has been investigated at DSDP Site 502A (Caribbean Sea) and DSDP Site 503A (Eastern Equatorial Pacific). Measurements were made of spire height (delta x), maximum diameter (delta y), the tangent angles of the upper and lower peripheral keels (phi 1, phi 2, respectively), the number of chambers in the final whorl, and the area of the silhouette in keel view. Four morphotypes alpha, beta, gamma, and delta were distinguished. Morphotype alpha was found in strata ranging in age from the Late Miocene through the Holocene. It shows a continuous increase in delta x and delta y until the Late Pleistocene. During and after the final closure of the ancient Central American Seaway (between 2.4 Ma and 1.8 Ma) there was a rapid increase in the area of the test in keel view. At the Caribbean Sea site, morphotype beta evolved during the past 0.22 Ma. It is less inflated than alpha and has a more delicate test. In the morphospace of delta x vs. delta y, morphotypes alpha and beta can be distinguished by a separation line delta y = 3.2 * delta x - 160 (delta x and delta y in µm). Plots of morphotype alpha are below that line, those of beta are above it. Morphotype alpha is taken to be Globorotalia menardii menardii Parker, Jones & Brady (1865) and includes G. menardii 'A' Bolli (1970). Morphotype beta is identified as G. menardii cultrata (d'Orbigny). Morphotypes gamma and delta are extinct Upper Miocene to Pliocene forms which evolved from morphotype alpha. They have a narrower phi 1 angle and more chambers (>=7) than morphotype alpha commonly with 5 to 6 chambers (7 in transitional forms). In contemporaneous samples morphotype delta can be distinguished from gamma by a smaller value of phi 1 and 8 or more chambers in the final whorl. Morphotype gamma is taken to be G. limbata (Fornasini, 1902) and includes the junior synonym G. menardii 'B' Bolli (1970). Morphotype delta is G. multicamerata Cushman & Jarvis (1930). With the exception of the Late Pleistocene development of G. menardii cultrataonly in the Caribbean the morphological changes of G. menardii at DSDP Sites 502A and 503A are similar. The development from the ancestral G. menardii menardii of the G. limbata - G. multicamerata lineage during the Pliocene and of G. menardii cultrata during the Late Pleistocene suggests responses at the two sites to a changing palaeoceanography during and after the formation of the Isthmus of Panama.

New alkaloids from Pandanus amaryllifolius

Three new alkaloids, the two pyrrolidine type alkaloids (1 and 2) and 6E-pandanamine (3), together with five known alkaloids (4-8), were isolated from the leaves of Pandanus amaryllifolius collected in West Java, Indonesia. All the new alkaloids have two alpha-methyl alpha,beta-unsaturated gamma-lactone moieties, while compound 2 also has an additional seven-membered ring, which has not been encountered before in Pandanus alkaloids. Two different extraction methods, namely, a solvent partitioning extraction and acid-base treatment, were tested, giving secondary and tertiary amines, respectively. Spectroscopic and chemical studies showed that the tertiary amines isolated from the acid-base treatment were artifacts formed during the extraction process. This finding suggests that the use of conventional acid-base treatment in isolating Pandanus alkaloids should be reviewed since it can introduce artifacts.

CTL recognition of a bulged viral peptide involves biased TCR selection

MHC class I molecules generally present peptides of 8-10 aa long, forming an extended coil in the HLA cleft. Although longer peptides can also bind to class I molecules, they tend to bulge from the cleft and it is not known whether the TCR repertoire has sufficient plasticity to recognize these determinants during the antiviral CTL response. In this study, we show that unrelated individuals infected with EBV generate a significant CTL response directed toward an HLA-B*3501-restricted, 11-mer epitope from the BZLF1 Ag. The 11-mer determinant adopts a highly bulged conformation with seven of the peptide side chains being solvent-exposed and available for TCR interaction. Such a complex potentially creates a structural challenge for TCR corecognition of both HLA-B*3501 and the peptide Ag. Surprisingly, unrelated B*3501 donors recognizing the 11-mer use identical or closely related alpha beta TCR sequences that share particular CDR3 motifs. Within the small number of dominant CTL clonotypes observed, each has discrete fine specificity for the exposed-side chain residues of the peptide. The data show that bulged viral peptides are indeed immunogenic but suggest that the highly constrained TCR repertoire reflects a limit to TCR diversity when responding to some unusual MHC peptide ligands.

Spongosoritin A: A new polyketide from a Fijian marine sponge, Spongosorites sp.

A new polyketide, spongosoritin A, with a rare vinylagous alpha,beta-unsaturated gamma-lactone moiety was isolated from a Fijian marine sponge, Spongosorites sp., and the structure assigned by detailed spectroscopic analysis.

The crystal structure of a bacterial Class II ketol-acid reductolsomerase: Domain conservation and evolution

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes two steps in the biosynthesis of branched-chain amino acids. Amino acid sequence comparisons across species reveal that there are two types of this enzyme: a short form (Class 1) found in fungi and most bacteria, and a long form (Class 11) typical of plants. Crystal structures of each have been reported previously. However, some bacteria such as Escherichia coli possess a long form, where the amino acid sequence differs appreciably from that found in plants. Here, we report the crystal structure of the E. coli enzyme at 2.6 A resolution, the first three-dimensional structure of any bacterial Class 11 KARI. The enzyme consists of two domains, one with mixed alpha/beta structure, which is similar to that found in other pyridine nucleotide-dependent dehydrogenases. The second domain is mainly alpha-helical and shows strong evidence of internal duplication. Comparison of the active sites between KARI of E. coli, Pseudomonas aeruginosa, and spinach shows that most residues occupy conserved positions in the active site. E. coli KARI was crystallized as a tetramer, the likely biologically active unit. This contrasts with P. aeruginosa KARI, which forms a dodecamer, and spinach KARI, a dimer. In the E. coli KARI tetramer, a novel subunit-to-subunit interacting surface is formed by a symmetrical pair of bulbous protrusions.

The human papillomavirus type 16 E7 protein binds human interferon regulatory factor-9 via a novel PEST domain required for transformation

It is critical that viruses are able to avoid the antiviral activities of interferon (IFN). We have shown previously that the human papillomavirus (HPV) is able to avoid IFN-alpha via interaction of the HPV-16 E7 protein with IFN regulatory factor-9 (IRF-9). Here, we investigated the details of the interaction using HPV-16 E7 peptide mapping to show that IRF-9 binds HPV-16 E7 in a domain encompassing amino acids 25-36. A closer examination of this region indicates this is a novel proline, glutamate, serine, and threonine-rich (PEST) domain, with a PEST score of 8.74. We have also mapped the region of interaction within IRF-9 and found that amino acids 354-393 play an important role in binding to HPV-16 E7. This region of IRF-9 encompasses the IRF association domain (IAD), a region important for protein-protein interaction central to IRF function. Finally, we used alanine-scanning mutagenesis to determine if E7-IRF-9 interaction was important for E7-mediated cellular transformation and found that the HPV-16 E7 mutants Y25A, E26A, S31A, S32A, and E35A, but not L28A and N29A, caused loss of transformation ability. Preliminary data suggest loss of IRF-9 interaction with E7 mutants correlated with transformation. Our work suggests E7- IRF- 9 interaction is important for the transforming ability of HPV-16 E7 and that HPV-16 E7 may interact with other IRF proteins that have IAD domains.

Biological, antigenic and phylogenetic characterization of the flavivirus Alfuy

Alfuy virus (ALFV) is classified as a subtype of the flavivirus Murray Valley encephalitis virus (MVEV); however, despite preliminary reports of antigenic and ecological similarities with MVEV, ALFV has not been associated with human disease. Here, it was shown that ALFV is at least 10(4)-fold less neuroinvasive than MVEV after peripheral inoculation of 3-week-old Swiss outbred mice, but ALFV demonstrates similar neurovirulence. In addition, it was shown that ALFV is partially attenuated in mice that are deficient in alpha/beta interferon responses, in contrast to MVEV which is uniformly lethal in these mice. To assess the antigenic relationship between these viruses, a panel of monoclonal antibodies was tested for the ability to bind to ALFV and MVEV in ELISA. Although the majority of monoclonal antibodies recognized both viruses, confirming their antigenic similarity, several discriminating antibodies were identified. Finally, the entire genome of the prototype strain of ALFV (MRM3929) was sequenced and phylogenetically analysed. Nucleotide (73%) and amino acid sequence (83 %) identity between ALFV and IMVEV confirmed previous reports of their close relationship. Several nucleotide and amino acid deletions and/or substitutions with putative functional significance were identified in ALFV, including the abolition of a conserved glycosylation site in the envelope protein and the deletion of the terminal dinucleotide 5'-CUOH-3' found in all other members of the genus. These findings confirm previous reports that ALFV is closely related to IMVEV, but also highlights significant antigenic, genetic and phenotypic divergence from MVEV. Accordingly, the data suggest that ALFV is a distinct species within the serogroup Japanese encephalitis virus.

Molecular recognition of an RNA trafficking element by heterogeneous nuclear ribonucleoprotein A2

Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a multitasking protein involved in RNA packaging, alternative splicing of pre-mRNA. telomere maintenance, cytoplasmic RNA trafficking, and translation. It binds short segments of single-stranded nucleic acids, including the A2RE11 RNA element that is necessary and sufficient for cytoplasmic transport of a subset of rnRNAs in oligodendrocytes and neurons. We have explored the structures of hnRNP A2, its RNA recognition motifs (RRMs) and Gly-rich module, and the RRM complexes with A2RE11. Circular dichroism spectroscopy showed that the secondary structure of the first 189 residues of hnRNP A2 parallels that of the tandem beta alpha beta beta alpha beta RRMs of its paralogue, hnRNP A1, previously deduced from X-ray diffraction studies. The unusual GRD was shown to have substantial beta-sheet and beta-turn structure. Sedimentation equilibrium and circular dichroism results were consistent with the tandem RRM region being monomeric and supported earlier evidence for the binding of two A2RE11 oligoribonucleotides to this domain, in contrast to the protein dimer formed by the complex of hnRNP A1 with the telomeric ssDNA repeat. A three-dimensional structure for the N-terminal, two-RRM-containing segment of hnRNP A2 was derived by homology modeling. This structure was used to derive a model for the complex with A2RE11 using the previously described interaction of pairs of stacked nucleotides with aromatic residues on the RRM beta-sheet platforms, conserved in other RRM-RNA complexes, together with biochemical data and molecular dynamics-based observations of inter-RRM mobility.

The displacement and strain field of three-dimensional rheologic model of earthquake preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.