Physical properties of ODP Leg 178 sites

We have reanalyzed the porosity, bulk density, and seismic velocity information collected from continental rise Sites 1095, 1096, and 1101 during the drilling of Ocean Drilling Program (ODP) Leg 178 (Fig. F1). The purpose is to provide a comprehensive composite digital set of data readily available for future studies aimed at well-seismic correlation. The work originates from the occurrence of overlapping sets of physical parameters and acoustic velocity collected by different methods (downhole logging, core logging, laboratory determination, and derivation from seismic data) and from different holes at the same site. These data do not always provide the same information because of difficulties encountered at each specific hole or methodological differences. In addition, a basic correlation between these parameters and onsite multichannel seismic (MCS) data is presented.

Strontium isotope geochemistry of ODP Leg 113 sites

The concentration of dissolved Sr and the distribution of 87Sr/86Sr isotope ratios in Leg 113 interstitial waters may be interpreted in terms of mixing of Sr from four different reservoirs: indigenous seawater, marine carbonate minerals, and basaltic and siliceous detrital material. The input to the pore water from these reservoirs is determined by the reactivity of the reservoir rather than its size. The presence of strontium derived from siliceous detrital material is unequivocally demonstrated in the pore waters of the hemipelagic deposits, and is also significant in the calcareous Maud Rise sediments due to the unusually low degree of carbonate recrystallization. Also, alteration of basic volcanic material is important at several sites.

Geochemistry of sands and sandstones in ODP Leg 126 sites

During Ocean Drilling Program Leg 126, six sites were cored in a young backarc rift basin and its flanks (rift onset 1.1-3.56 Ma) and in the forearc basin of the Izu-Bonin Arc. In the backarc area, strata are younger than about 4.5 Ma, whereas in the forearc, ages are about 0-31 Ma in sections punctuated by important Miocene unconformities. Bulk chemical analyses of volcaniclastic turbidite sands and sandstones, derived directly from the arc, were obtained from 271 atomic absorption analyses (major elements), 253 XRF analyses (trace elements) and 16 ICP-MS analyses (trace and rare-earth elements). Of the 271 samples, 78 come from the backarc area and the remainder from the forearc. The sands and sandstones reflect the igneous compositions of their sources. Most are formed of materials derived from subalkaline, low-K andesites, and dacites, although compositions range from basalt to rhyolite. Basic and acid andesites are predominant in Oligocene rocks; in contrast, Pliocene-Pleistocene sediments were derived from acid andesitic to rhyolitic sources. The oldest sandstones, estimated to have an age of about 31 Ma, were derived from an arc tholeiitic, not boninitic, source. The 26-31 Ma sandstones furthest to the north, at Sites 787 and 792, have higher relative concentrations of Ti, Zr, and Y than do those at southern Site 793. Data from younger samples indicate that, for more than 30 m.y., the average composition of volcaniclastic sediments and volcanism near Aoga Shima was more basic than to the south, near Sumisu Jima. Using the sandstones as igneous proxies, we conclude that magmas erupted along the arc have become more depleted in light-rare-earth elements (LREE) with time. There was a major change in rare-earth-element (REE) concentrations in the late Oligocene, from essentially flat patterns (normalized La/Yb about 1-1.5) to LREE-depleted patterns (normalized La/Yb about 0.5). At the same time, Zr/Y ratios decreased from about 2-4 to about 1.5-2.5. These changes may reflect a shift in provenance, or changes in the composition of the mantle wedge beneath the arc. In the backarc area, lithic clasts and glass shards of rift-facies basalt are present in sediments as old as 2.35-3.15 Ma. Two samples of mafic sand from the backarc basin have flat REE patterns (normalized La/Yb about 1.0), like some of the <1-Ma rift lavas and unlike pre-rift sand and sandstone samples. These possibly represent the local effects of sedimentary mixing of detritus from arc and backarc eruptions because no evidence from the arc itself exists to suggest a recent change in the REE content of magmas.

Amino acids in interstitial waters from ODP Sites 126-790 and 126-791

Sites 790 and 791 lie in the eastern half graben of the Sumisu Rift, a backarc graben west of the active Izu-Bonin arc volcanoes Sumisu Jima and Tori Shima, at 30°54.96'N, 139°50.66'E, in 2223 m water depth and 30°54.97'N, 139°52.20'E, in 2268 m water depth, respectively. A small decrease in the sulfate concentration in the interstitial waters from these sites suggests fairly low microbial activity by sulfate-reducing bacteria. The values of the dissolved free amino acids (DFAA) in the interstitial waters from both sites range from 1.26 to 6.82 µmol/L, with an average of 3.81 µmol/L. The acidic, basic, neutral, aromatic, and sulfur-containing amino acids have average values of 0.32, 0.50, 2.71, 0.15, and 0.09 µmol/L, respectively. The relative abundances of the acidic, basic, neutral, aromatic, and sulfur-containing amino acids average 8, 13,72, 4, and 1 mol%, respectively. Glycine, serine, alanine, ornithine, and aspartic acid are major constituent amino acids. The dissolved combined amino acids (DCAA) values range between 1.25 and 44.35 µmol/L, with an average of 10.36 µmol/L. The mean concentrations and relative abundances of the acidic, basic, neutral, aromatic, and sulfur-containing amino acids are 2.29 (22 mol%), 0.60 (6 mol%), 6.70 (65 mol%), 0.09 (1 mol%), and 0.00 µmol/L (0 mol%), respectively. Glycine is the most abundant amino acid residue, followed by glutamic acid, serine, and alanine. The predominance of DCAA over DFAA present in the interstitial waters from Sites 790 and 791 is consistent with previous results from interstitial-water and seawater analyses. The most plausible source for the DCAA is biogenic calcareous debris. A much greater depletion of aspartic acid and the basic fraction, except for ornithine, is found in the DCAA. The decomposition of the basic amino acid fraction or its incorporation to clay minerals would result in a decrease in its relative abundance, whereas ornithine is produced during early diagenesis. The characteristics of the amino acids in the interstitial waters are (1) a greater depletion of the acidic amino acid fraction in the DFAA than in the DCAA and (2) the enrichment of glycine and serine in both. The adsorption or reaction of the amino acids in interstitial waters with biogenic carbonates would be responsible for the lower relative abundance of the acidic fraction of the DFAA. The production of glycine during early diagenesis and its stability in solution would raise its relative abundance in the interstitial waters.

Mineral composition, major element oxides and trace element concentration of sediments from ODP Leg 180 sites

Middle Miocene to Holocene fine-grained argillaceous sediments (clays, claystones/muds, and mudstones), which volumetrically dominated the sediment recovery in the Woodlark Basin during Leg 180, were chemically analyzed for major elements, trace elements, and some rare earth elements by X-ray fluorescence. Selected samples also underwent X-ray diffraction (XRD) analysis for mineral determination. The results shed light on sediment provenance when combined with shipboard sediment descriptions, smear slide study, and XRD. The oldest sediments recovered (Site 1108) of middle-late Miocene age include volcanogenic muds with distinctive high MgO and K2O, indicative of a relatively basic calc-alkaline source related to an inferred Miocene forearc succession. The forearc basement, composed of diabase and basalt, was locally exposed (Site 1109) and eroded in the late Miocene (<5.4-9.93 Ma), giving rise to fluvial conglomerates (Sites 1109, 1115, and 1118). Chemically distinctive fine-grained claystones and siltstones (with relatively high Ti, low K) are compatible with derivation from tropically weathered basic igneous rocks, correlated with the Paleogene Papuan ophiolite. Overlying latest Miocene-Pleistocene fine-grained sediments throughout the Woodlark Basin were partly derived from calc-alkaline volcanic sources. However, relatively high abundances of Al2O3 and related element oxides (K2O and Na2O) and trace elements (e.g., Rb and Y) reflect an additional terrigenous input throughout the basin, correlated with pelitic metamorphic rocks exposed on Papua New Guinea and adjacent areas. In addition, sporadic high abundances of Cr and Ni, some other trace metals, and related minerals (talc, crysotile, and chlorite) reflect input from an ophiolitic terrain dominated by ultramafic rocks, correlated with the Paleogene Papuan ophiolite. The source areas possibly included serpentinized ultramafic ophiolitic rocks exposed in the Papua New Guinea interior highlands. Chemical evidence further indicates that fine-grained terrigenous sediment reached the Woodlark Basin throughout its entire late Miocene-Holocene history. Distinctive high-K volcanogenic muds rich in tephra and volcanic ash layers that appear at <2.3 Ma (Sites 1109 and 1115) are indicative of high-K calc-alkaline volcanic centers, possibly located in the Dawson Strait, Moresby Strait, or Dobu Seamount area. Chemical diagenesis of fine-grained sediments within the Woodlark Basin is reflected in clay neomorphism and localized formation of minerals including dolomite, ankerite, and zeolite but has had little effect on the bulk chemical composition of most samples.

Organic carbon and humic substances contents, carbon isotope composition and peroxidase activity in sediments from DSDP Sites 15-147 and 75-532

Sediment samples from the Cariaco Trench (DSDP Leg 15) and the Walvis Ridge (DSDP Leg 75) ranging in age from Holocene to Upper Miocene (approximately 8 million years BP) and in depth from 5 to 258 m were extracted with basic sodium pyrophosphate and the extract analyzed for enzymic activity. Since no dehydrogenase, alkaline phosphatase or esterase activity was found, it is estimated from these data that the maximum bacterial population does not exceed 1000 cells per gram dry sediment. Peroxidase activity was, however, found in most samples: this showed marked dependence on the humic substance concentration (expressed as percent of the organic carbon content) and increased with depth at a rate of 33 units per meter. To explain this observation, we favor an hypothesis based on the presence of active humic-enzyme association. The humic substances absorb and stabilize peroxidase which is liberated throughout the sediment column by lysis of cells. The association of the enzyme with the humic substances protects it from biodegradation and denaturation. This hypothesis agrees with laboratory experiments which show the enhanced stability of humic-enzyme complexes towards degradation by biological, chemical and thermal effects.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos–Jun–AP-1 complex may contribute to its functional versatility at different promoters.

Characterization and tissue-specific expression of the rat basic fibroblast growth factor antisense mRNA and protein

An RNA transcribed from the antisense strand of the FGF-2 gene has been implicated in the regulation of FGF-2 mRNA stability in amphibian oocytes. We have now cloned and characterized a novel 1.1-kb mRNA (fgf-as) from neonatal rat liver. In non-central nervous system (CNS) tissues the fgf-as RNA is abundantly expressed in a developmentally regulated manner. The FGF-AS cDNA contains a consensus polyadenylylation signal and a long open reading frame (ORF) whose deduced amino acid sequence predicts a 35-kDa protein with homology to the MutT family of nucleotide hydrolases. Western blot analysis with antibodies against the deduced peptide sequence demonstrates that the FGF-AS protein is expressed in a broad range of non-CNS tissue in the postnatal period. In the developing brain, the abundance of sense and antisense transcripts are inversely related, suggesting a role for the antisense RNA in posttranscriptional regulation of FGF-2 expression in this tissue.The FGF-AS is complementary to two widely separated regions in the long 3′ untranslated region of the FGF-2 mRNA, in the vicinity of the proximal and distal polyadenylylation sites. These findings demonstrate that the FGF-2 and fgf-as RNAs are coordinately transcribed on a tissue-specific and developmentally regulated basis and suggest that interaction of the sense and antisense RNAs may result in posttranscriptional regulation of FGF-2 in some tissues.

Premature Polyadenylation at Multiple Sites within a Bacillus thuringiensis Toxin Gene-Coding Region1

Some foreign genes introduced into plants are poorly expressed, even when transcription is controlled by a strong promoter. Perhaps the best examples of this problem are the cry genes of Bacillus thuringiensis (B.t.), which encode the insecticidal proteins commonly referred to as B.t. toxins. As a step toward overcoming such problems most effectively, we sought to elucidate the mechanisms limiting the expression of a typical B.t.-toxin gene, cryIA(c), which accumulates very little mRNA in tobacco (Nicotiana tabacum) cells. Most cell lines transformed with the cryIA(c) B.t.-toxin gene accumulate short, polyadenylated transcripts. The abundance of these transcripts can be increased by treating the cells with cycloheximide, a translation inhibitor that can stabilize many unstable transcripts. Using a series of hybridizations, reverse-transcriptase polymerase chain reactions, and RNase-H-digestion experiments, poly(A+) addition sites were identified in the B.t.-toxin-coding region corresponding to the short transcripts. A fourth polyadenylation site was identified using a chimeric gene. These results demonstrate for the first time to our knowledge that premature polyadenylation can limit the expression of a foreign gene in plants. Moreover, this work emphasizes that further study of the fundamental principles governing polyadenylation in plants will have basic as well as applied significance.

Preferential self-association of basic fibroblast growth factor is stabilized by heparin during receptor dimerization and activation.

Central to signaling by fibroblast growth factors (FGFs) is the oligomeric interaction of the growth factor and its high-affinity cell surface receptor, which is mediated by heparin-like polysaccharides. It has been proposed that the binding of heparin-like polysaccharides to FGF induces a conformational change in FGF, resulting in the formation of FGF dimers or oligomers, and this biologically active form is 'presented' to the FGF receptor for signal transduction. In this study, we show that monomeric basic FGF (FGF-2) preferentially self-associates and forms FGF-2 dimers and higher-order oligomers. As a consequence, FGF-2 monomers are oriented for binding to heparin-like polysaccharides. We also show that heparin-like polysaccharides can readily bind to self-associated FGF-2 without causing a conformational change in FGF-2 or disrupting the FGF-2 self-association, but that the bound polysaccharides only additionally stabilize the FGF-2 self-association. The preferential self-association corresponds to FGF-2 translations along two of the unit cell axes of the FGF-2 crystal structures. These two axes represent the two possible heparin binding directions, whereas the receptor binding sites are oriented along the third axis. Thus, we propose that preferential FGF-2 self-association, further stabilized by heparin, like "beads on a string," mediates FGF-2-induced receptor dimerization and activation. The observed FGF-2 self-association, modulated by heparin, not only provides a mechanism of growth factor activation but also represents a regulatory mechanism governing FGF-2 biological activity.

Elicitins from Phytophthora and basic resistance in tobacco.

Elicitins are a family of small proteins secreted by species of Phytophthora. They are thought to be major determinants of the resistance response of tobacco against these oomycetes, since purified elicitins, alone and at low concentrations, can induce vigorous defense responses in tobacco (i.e., hypersensitive cell death and resistance against subsequent pathogen attack), and in vitro elicitin production by Phytophthora isolates is strongly negatively correlated with their pathogenicity on tobacco plants. A number of elicitins have been purified and their amino acid sequences have been determined and found to be conserved. A three-dimensional structure for elicitin is emerging from nuclear magnetic resonance studies. Two structural classes, alpha and beta, are distinguished by their biological effects when applied to decapitated stems or petioles; the beta class causes more necrosis on leaves and provides better subsequent protection against pathogen attack. However, both these classes of elicitins will similarly cause necrosis when each is, instead, directly infiltrated into tobacco leaf panels. Effects of elicitins on tobacco cells include rapid electrolyte leakage, changes in protein phosphorylation and amounts of active oxygen species, and later production of ethylene and capsidiol. The sites of initial interaction with tobacco cells are unknown, but the interaction appears to induce general defense-related responses.

The hepatitis B virus X protein targets the basic region-leucine zipper domain of CREB.

The X gene product encoded by the hepatitis B virus, termed pX, is a promiscuous transactivator of a variety of viral and cellular genes under the control of diverse cis-acting elements. Although pX does not appear to directly bind DNA, pX-responsive elements include the NF-kappa B, AP-1, and CRE (cAMP response element) sites. Direct protein-protein interactions occur between viral pX and the CRE-binding transcription factors CREB and ATF. Here we examine the mechanism of the protein-protein interactions occurring between CREB and pX by using recombinant proteins and in vitro DNA-binding assays. We demonstrate that pX interacts with the basic region-leucine zipper domain of CREB but not with the DNA-binding domain of the yeast transactivator protein Gal4. The interaction between CREB and pX increases the affinity of CREB for the CRE site by an order of magnitude, although pX does not alter the rate of CREB dimerization. Methylation interference footprinting reveals differences between the CREB DNA and CREB-pX DNA complexes. These experiments demonstrate that pX titers the way CREB interacts with the CRE DNA and suggest that the basic, DNA-binding region of CREB is the target of pX. Transfection assays in PC12 cells with the CREB-dependent somatostatin promoter demonstrate a nearly 15-fold transcriptional induction after forskolin stimulation in the presence of pX. These results support the significance of the CREB-pX protein-protein interactions in vivo.

Geochemistry of labile organic matter in sediments and interstitial waters of ODP Sites 107-651 and 107-653

Sediment and interstitial water from Sites 651 and 653 (ODP Leg 107) were investigated by organic geochemical methods to characterize labile organic compound classes (amino compounds and carbohydrates) and to evaluate their progressive diagenetic and thermal degradation in deep-sea sediments. Downhole distribution of dissolved organic carbon (DOC) appears related to redox zones associated with bacterial activity and of diagenetic recrystallization of biogenic tests and not so much to organic matter concentrations in ambient sediments. DOC ranges from 250 to 8300 µmol/L (3-100.1 ppm). Amino acids contribute 10%-0.3% of DOC; carbohydrates range from 78 to 5 µmol/L. Rate of degradation of amino acids by thermal effects and/or bacterial activity at both sites (significantly different in sedimentation rates: average 41 cm/1000 yr in the top 300 m at Site 651, average 3.9 cm/1000 yr in the Pliocene/Quaternary sequence at Site 653 to 220 mbsf) is more dependent on exposure time rather than on the depth within the sediment column. Variability in neutral, acidic, and basic amino acid fractions of total amino acids (with a range of 1.1-0.02 µmol/g sediment; up to 2.5% of organic carbon) varies with carbonate content and by differences in thermal stability of amino acids. Distribution patterns of monosaccharides are interpreted to result from differences in organic matter sources, sedimentation rates, and the degree of organic matter decomposition prior to and subsequent to burial. Total particulate carbohydrates range from 1.82 to 0.21 µmol/g sediment and contribute about 8% to the sedimentary organic matter. Investigation of trace metals in the interstitial waters did not show any correlation of either DOC, amino compounds, or carbohydrates.

Lithology and approximate sub-bottom depths and ages of the transition of soft to firm ooze and of firm ooze to chalk at DSDP Leg 89 and 90 Sites

Leg 90 recovered approximately 3705 m of core at eight sites lying at middle bathyal depths (1000-2200 m) (Sites 587 to 594) in a traverse from subtropical to subantarctic latitudes in the southwest Pacific region, chiefly on Lord Howe Rise in the Tasman Sea. This chapter summarizes some preliminary lithostratigraphic results of the leg and includes data from Site 586, drilled during DSDP Leg 89 on the Ontong-Java Plateau that forms the northern equatorial point of the latitudinal traverse. The lithofacies consist almost exclusively of continuous sections of very pure (>95% CaCO3) pelagic calcareous sediment, typically foraminifer-bearing nannofossil ooze (or chalk) and nannofossil ooze (or chalk), which is mainly of Neogene age but extends back into the Eocene at Sites 588, 592, and 593. Only at Site 594 off southeastern New Zealand is there local development of hemipelagic sediments and several late Neogene unconformities. Increased contents of foraminifers in Leg 90 sediments, notably in the Quaternary interval, correspond to periods of enhanced winnowing by bottom currents. Significant changes in the rates of sediment accumulation and in the character and intensity of sediment bioturbation within and between sites probably reflect changes in calcareous biogenic productivity as a result of fundamental paleoceanographic events in the region during the Neogene. Burial lithification is expressed by a decrease in sediment porosity from about 70 to 45% with depth. Concomitantly, microfossil preservation slowly deteriorates as a result of selective dissolution or recrystallization of some skeletons and the progressive appearance of secondary calcite overgrowths, first about discoasters and sphenoliths, and ultimately on portions of coccoliths. The ooze/chalk transition occurs at about 270 m sub-bottom depth at each of the northern sites (Sites 586 to 592) but is delayed until about twice this depth at the two southern sites (Sites 593 and 594). A possible explanation for this difference between geographic areas is the paucity of discoasters and sphenoliths at the southern sites; these nannofossil elements provide ideal nucleation sites for calcite overgrowths. Toward the bottom of some holes, dissolution seams and flasers appear in recrystallized chalks. The very minor terrigenous fraction of the sediment consists of silt- through clay-sized quartz, feldspar, mica, and clay minerals (smectite, illite, kaolinite, and chlorite), supplied as eolian dust from the Australian continent and by wind and ocean currents from erosion on South Island, New Zealand. Changes in the mass accumulation rates of terrigenous sediment and in clay mineral assemblages through time are related to various external controls, such as the continued northward drift of the Indo-Australian Plate, the development of Antarctic ice sheets, the increased desertification of the Australian continent after 14 m.y. ago, and the progressive increase in tectonic relief of New Zealand through the late Cenozoic. Disseminated glass shards and (altered) tephra layers occur in Leg 90 cores. They were derived from major silicic eruptions in North Island, New Zealand, and from basic to intermediate explosive volcanism along the Melanesian island chains. The tephrostratigraphic record suggests episodes of increased volcanicity in the southwest Pacific centered near 17, 13, 10, 5 and 1 m.y. ago, especially in the middle and early late Miocene. In addition, submarine basaltic volcanism was widespread in the southeast Tasman Sea around the Eocene/Oligocene boundary, possibly related to the propagation of the Southeast Indian Ridge through western New Zealand as a continental rift system.

Toward better adjusted children; basic principles underlying a pupil personnel program.

Mode of access: Internet.