Chromatin structure and DNase I hypersensitivity in the transcriptionally active and inactive porcine tumor necrosis factor gene locus

We have analyzed the chromatin structure of the porcine tumor necrosis factor gene locus (TNF-alpha and TNF-beta). Nuclei from porcine peripheral blood mononuclear cells were digested with different nucleases. As assessed with micrococcal nuclease, the two TNF genes displayed slightly faster digestion kinetics than bulk DNA. Studies with DNaseI revealed distinct DNaseI hypersensitive sites (DH-sites) within the porcine TNF locus. Four DH-sites could be observed in the promoter and mRNA leader regions of the TNF-beta gene. Two DH-sites could be observed for the TNF-alpha gene, one located in the promoter region close to the TATA-box and the other site in intron 3. This pattern of DH-sites was present independently of the activation state of the cells. Interestingly in a porcine macrophage-like cell line, we found that the TNF-alpha promoter DH-site disappeared and another DH-site appeared in the region of intron 1. Additionally, the DH-site of intron 3 could be enhanced by PMA-stimulation in these cells. TNF-beta sites were not detected in this cell line. However, DH-sites were totally absent in fibroblasts (freshly isolated from testicles) and in porcine kidney cells (PK15 cell line) both of which do not transcribe the TNF genes. Therefore, the pattern of DH-sites corresponds to the transcriptional activity of analyzed cells.

The low abundance of U7 snRNA is partly determined by its Sm binding site.

In transient expression studies after DNA transfection of HeLa cells, the mouse U7 gene produces only approximately 30% of the RNA produced by a mouse U1b gene. This difference persists even when the transfected genes have all their 5' and 3' flanking sequences exchanged suggesting a post-transcriptional effect. When the special U7 Sm binding site is mutated to a consensus derived from the major snRNAs (Sm-opt), the U7 RNA level increases 4- to 5-fold, whereas no RNA is detected from a U7 gene with a non-functional Sm binding site (Sm-mut). Moreover, U1b genes with the U7 Sm binding site yield reduced RNA levels. The Sm-opt site also alters the cellular behaviour of the corresponding U7 snRNA. It accumulates to a higher level in the nucleus than wild type U7 RNA, and is better immunoprecipitable with anti-Sm antibodies. Injection experiments in Xenopus oocytes indicate that the U7 genes with either Sm-opt or Sm-mut sites produce similar amounts of RNA as wild type U7, but that they differ in opposing ways in the processing of precursors to mature size U7 snRNA and in nuclear accumulation. However, in reconstitution experiments using Xenopus oocytes, we show that U7 Sm-opt RNA, despite its efficient nuclear accumulation, is not active in 3' processing of histone pre-mRNA, whereas wild type U7 RNA is assembled into functional snRNPs, which correctly process histone pre-mRNA substrate. This suggests a functional importance of the special U7 Sm sequence.

(Table 1) U and Th isotope analyses of pyrite and anhydrite of ODP Site 158-957

Hydrothermal circulation at oceanic spreading ridges causes sea water to penetrate to depths of 2 to 3 km in the oceanic crust where it is heated to ~400 °C before venting at spectacular 'black smokers'. These hydrothermal systems exert a strong influence on ocean chemistry (Edmond et al., 1979, doi:10.1016/0012-821X(79)90061-X), yet their structure, longevity and magnitude remain largely unresolved (Elderfield and Schultz., 1996, doi:10.1146/annurev.earth.24.1.191). The active Transatlantic Geotraverse (TAG) deposit, at 26° N on the Mid-Atlantic Ridge, is one of the largest, oldest and most intensively studied of the massive sulphide mounds that accumulate beneath black-smoker fields. Here we report ages of sulphides and anhydrites from the recently drilled (Humphris et al., 1995, doi:10.1038/377713a0) TAG substrate structures -determined from 234U-230Th systematics analysed by thermal ionization mass spectrometry. The new precise ages combined with existing data (Lalou et al., 1993, doi:10.1029/92JB01898; 1998, doi:10.2973/odp.proc.sr.158.214.1998) show that the oldest material (11,000 to 37,000 years old) forms a layer across the centre of the deposit with younger material (2,300-7,800 years old) both above and below. This stratigraphy confirms that much of the sulphide and anhydrite are precipitated within the mound by mixing of entrained sea water with hydrothermal fluid (James and Elderfield, 1996, doi:10.1130/0091-7613(1996)024<1147:COOFFA>2.3.CO;2). The age distribution is consistent with episodic activity of the hydrothermal system recurring at intervals of up to 2,000 years.

Potassium and argon concentrations and age determination of ODP Site 125-782 and 125-786

K-Ar whole-rock ages have been obtained for 30 samples from Sites 782 and 786, Ocean Drilling Program Leg 125 in the Izu-Bonin (Ogasawara) forearc region. They form a trimodal spread of ages between 9 Ma and 44 Ma and are, with a few exceptions, consistent with the inferred lithostratigraphy. The ages have been interpreted in terms of at least two distinct episodes of magmatic and/or hydrothermal activity. A group of ten samples, including the lava flows, gave an isochron age of 41.3 ± 0.5 Ma (middle-late Eocene). This is thought to represent the age of the principal magmatic development of the volcanic forearc basement, and is comparable to published ages on equivalent rocks from other parts of the forearc basement high (e.g., the Ogasawara Islands). It may be significant that this age is slightly younger than the timing of major plate reorganization in the Western Pacific at about 43 Ma. This was followed by a minor episode of intrusive magmatism at 34.6 ± 0.7 Ma (early Oligocene) which appears to have reset the ages of some of the earlier units. This event probably corresponds to the initiation of rifting of the "proto-arc" to form the Parece Vela Basin. Boninitic samples were erupted during both episodes of magmatism, the earlier being of low-Ca boninite type and the later being of medium- and high-Ca types. It is also possible that a third episode of intrusive magmatism affected the Izu-Bonin forearc region at both Sites 782 and 786 at about 17 Ma. This would be consistent with magmatic activity elsewhere in the region during the Miocene, associated with the end of active spreading in the Parece Vela Basin and the start of arc activity in the West Mariana Ridge.

(Table 1) Organic geochemistry of ODP Hole 134-832B and Site 134-833

Ocean Drilling Program (ODP) Leg 134 was located in the central part of the New Hebrides Island Arc, in the Southwest Pacific. Here the d'Entrecasteaux Zone of ridges, the North d'Entrecasteaux Ridge and South d'Entrecasteaux Chain, is colliding with the arc. The region has a Neogene history of subduction polarity reversal, ridge-arc collision, and back-arc spreading. The reasons for drilling in this region included the following: (1) to determine the differences in the style and time scale of deformation associated with the two ridge-like features (a fairly continuous ridge and an irregularly topographic seamount chain) that are colliding with the central New Hebrides Island Arc; (2) to document the evolution of the magmatic arc in relation to the collision process and possible Neogene reversal of subduction; and (3) to understand the process of dewatering of a small accretionary wedge associated with ridge collision and subduction. Seven sites were occupied during the leg, five (Sites 827-831) were located in the d'Entrecasteaux Zone where collision is active. Three sites (Sites 827, 828, and 829) were located where the North d'Entrecasteaux Ridge is colliding, whereas two sites (Sites 830 and 831) were located in the South d'Entrecasteaux Chain collision zone. Sites 828 (on North d'Entrecasteaux Ridge) and 831 (on Bougainville Guyot) were located on the Pacific Plate, whereas all other sites were located on a microplate of the North Fiji Basin. Two sites (Sites 832 and 831) were located in the intra-arc North Aoba Basin. Results of Leg 134 drilling showed that forearc deformation associated with the North d'Entrecasteaux Ridge and South d'Entrecasteaux Chain collision is distinct and different. The d'Entrecasteaux Zone is an Eocene subduction/obduction complex with a distinct submerged island arc. Collision and subduction of the North d'Entrecasteaux Ridge results in off scraping of ridge material and plating of the forearc with thrust sheets (flakes) as well as distinct forearc uplift. Some offscraped sedimentary rocks and surficial volcanic basement rocks of the North d'Entrecasteaux Ridge are being underplated to the New Hebrides Island forearc. In contrast, the South d'Entrecasteaux Chain is a serrated feature resulting in intermittent collision and subduction of seamounts. The collision of the Bougainville Guyot has indented the forearc and appears to be causing shortening through thrust faulting. In addition, we found that the Quaternary relative convergence rate between the New Hebrides Island Arc at the latitude of Espiritu Santo Island is as high as 14 to 16 cm/yr. The northward migration rate of the d'Entrecasteaux Zone was found the be ~2 to 4 cm/yr based on the newly determined Quaternary relative convergence rate. Using these rates we established the timing of initial d'Entrecasteaux Zone collision with the arc at ~3 Ma at the latitude of Epi Island and fixed the impact of the North d'Entrecasteaux Ridge upon Espiritu Santo Island at early Pleistocene (between 1.89 and 1.58 Ma). Dewatering is occurring in the North d'Entrecasteaux Ridge accretionary wedge, and the wedge is dryer than other previously studied accretionary wedges, such as Barbados. This could be the result of less sediment being subducted at the New Hebrides compared to the Barbados.

Granulometry, mineralogy and geochemistry of sediments from ODP Hole 169-1037B and Site 169-1038

Central Hill is in the northern part of the Escanaba Trough, which is a sediment-filled rift of southern Gorda Ridge. Central Hill is oriented north-south and is associated with extensive sulfide deposits. Hydrothermal alteration of sediment from Site 1038 was studied through analyses of mineralogy and the chemistry and oxygen isotopic compositions of one nearly pure clay sample. In addition, Site 1037 was drilled to establish the character of the unaltered sedimentary sequence away from the hydrothermal centers of the Northern Escanaba Trough Study Area (NESCA). Mineralogy of the clay-size fraction of turbiditic and hemipelagic sediments of Hole 1037B are predominantly quartz, feldspar, pyroxene, illite, chlorite, and smectite, representing continental-derived material. Cores from Hole 1038I, located within the area of Central Hill but away from known active vent areas, recovered minor amounts of chlorite/smectite mixed-layer clay in the fine fraction, indicating a low-temperature hydrothermal alteration. The 137.4-m-thick sediment section of Hole 1038G is located in an area of low-temperature venting. The uppermost sample is classified as chlorite/smectite mixed layer, which is underlain by chlorite as the dominant mineral. The lowermost deposits of Hole 1038G are also characterized by chlorite/smectite mixed-layer clay. In comparison to Hole 1038I, the mineralogic sequence of Hole 1038G reflects increased chloritization. Intensely altered sediment is almost completely replaced by hydrothermal chlorite in subsurface sediments of Hole 1038H. Alteration to chlorite is characterized by depletion in Na, K, Ti, Ca, Sr, Cs, and Tl and enrichment in Ba. Further, Eu depletion reflects a high-temperature plagioclase alteration. A chlorite 18O value of 2.6 indicates formation at a temperature of ~190°C. It is concluded that the authigenic chlorite in Hole 1038H formed by an active high-temperature fluid flow in the shallow subsurface.

Stable oxygen isotopes of calcite veins in ODP Site 146-892

In situ secondary ionization mass spectrometry (SIMS) analyses of oxygen isotopes in authigenic calcite veins were obtained from an active thrust fault system drilled at Ocean Drilling Program (ODP) Site 892 (44°40.4'N, 125°07.1'W) along the Cascadia subduction margin. The average d18OPDB value of all samples is -9.9 per mil and the values are the lowest of any measured in active accretionary prisms. Ranges in individual veins can be as much as 19.6 per mil. There is an isotopic stratigraphy related to the structural stratigraphy. Mean isotope values in the hanging wall, thrust, and footwall are -14.4 per mil, -9.5 per mil, and -5.2 per mil, respectively. Several veins and crosscutting vein sequences show a general trend from lower to higher d18O values over time. Isotopic and textural data indicate several veins formed by a crack-seal mechanism and growth into open fractures. The best explanation for the strong 18O depletions is periodic rapid flow from 2-3 km deeper in the prism. Relatively narrow isotopic ranges for most veins suggest that fluids were derived from a similar source depth for each episode of fluid pulse and calcite crystallization. Structural and mass balance considerations are consistent with a record preserved in the veins of ten to hundreds of thousands of years. The fluid pulses may relate to periodic large earthquake events such as those recognized in the paleoseismicity records from the Cascadia margin.

Petrology and geochemistry at DSDP Site 59-448

This chemical and petrologic study of rocks from Site 448 on the Palau-Kyushu Ridge is designed to answer some fundamental questions concerning the volcanic origin of remnant island arcs. According to the reconstruction of the Western Pacific prior to about 45 m.y. ago (Hilde et al., 1977), the site of the Palau-Kyushu Ridge was a major transform fault. From a synthesis of existing geological and geophysical data (R. Scott et al., this volume), it appears that the ridge originated by subduction of the Pacific plate under the West Philippine Basin. Thus the Palau-Kyushu Ridge should be a prime example of both initial volcanism of an incipient arc formed by interaction of oceanic lithospheric plates and remnant-arc volcanic evolution. The Palau-Kyushu Ridge was an active island arc from about 42 to 30 m.y. ago, after which initiation of back-arc spreading formed the Parece Vela Basin (R. Scott et al., this volume; Karig, 1975a). This spreading left the western portion of the ridge as a remnant arc that separates the West Philippine Basin from the Parece Vela Basin. In spite of numerous oceanographic expeditions to the Philippine Sea, including the two previous DSDP Legs 6 and 31 (Fischer, Heezen et al., 1971; Karig, Ingle et al., 1975), and even though the origins of inter-arc basins have been linked by various hypotheses to that of remnant island arcs (Karig, 1971, 1972, 1975a, and 1975b; Gill, 1976; Uyeda and Ben-Avraham, 1972; Hilde et al., 1977), very little hard data are available on inactive remnant arcs.

Turbiditic trench deposits at the South-Chilean active margin

The active plate margin of South America is characterized by a frequent occurrence of large and devastating subduction earthquakes. Here we focus on marine sedimentary records off Southern Chile that are archiving the regional paleoseismic history over the Holocene and Late Pleistocene. The investigated records - Ocean Drilling Program (ODP) Site 1232 and SONNE core 50SL - are located at ~40°S and ~38°S, within the Perú-Chile trench, and are characterized by frequent interbedded strata of turbiditic and hemipelagic origin. On the basis of the sedimentological characteristics and the association with the active margin of Southern Chile, we assume that the turbidites are mainly seismically triggered, and may be considered as paleo-megaearthquake indicators. However, the long-term changes in turbidite recurrence times appear to be strongly influenced by climate and sea level changes as well. During sea level highstands in the Holocene and Marine Isotope Stage (MIS) 5, recurrence times of turbiditic layers are substantially higher, primarily reflecting a climate-induced reduction of sediment availability and enhanced slope stability. In addition, segmented tectonic uplift changes and related drainage inversions likely influenced the postglacial decrease in turbidite frequencies. Glacial turbidite recurrence times (including MIS 2, MIS 3, cold substages of MIS 5, and MIS 6), on the other hand, are within the same order of magnitude as earthquake recurrence times derived from the historical record and other terrestrial paleoseismic archives of the region. Only during these cold stages sediment availability and slope instability were high enough to enable recording of the complete sequence of large earthquakes in Southern Chile. Our data thus suggest that earthquake recurrence times on the order of 100 to 200 years are a persistent feature at least during the last glacial period.

Chemistry of smectite and volcanic glass of ODP Site 159-959

The Ocean Drilling Program (ODP) Site 959 was drilled in the northern border of the Côte d'Ivoire-Ghana Ridge at a water depth of 2100 m. Pleistocene total thickness does not exceed 20 m. Winnowing processes resulted in a low accumulation rate and notable stratigraphic hiatuses. During the Late Pleistocene, bottom circulation was very active and controlled laminae deposition (contourites) which increased the concentration of glauconitic infillings of foraminifera, and of volcanic glass and blue-green grains more rarely, with one or several subordinate ferromagnesian silicates. Volcanic glass generally was X-ray amorphous and schematically classified as basic to intermediate (44-60% SiO2). Opal-A or opal-CT suggested the beginning of the palagonitisation process, and previous smectitic deposits may have been eroded mechanically. The blue-green grains presented two main types of mineralogic composition: (1) neoformed K, Fe-smectite associated with zeolite (like phillipsite) and unequal amounts of quartz and anorthite; (2) feldspathic grains dominated by albite but including quartz, volcanic glass and smectites as accessory components. They were more or less associated with the volcanic glass. On the basis of their chemical composition, the genetic relationship between the blue-green grains and the volcanic glass seemed to be obvious although some heterogeneous grains seemed to be primary ignimbrite and not the result of glass weathering. The most reasonable origin of these pyroclastic ejecta would be explosive events from the Cameroon Volcanic Ridge, especially from the Sao Thome and Principe Islands and Mount Cameroon area. This is supported both by grain geochemistry and the time of volcanic activity, i.e. Pleistocene. After westward wind transport (some 1200 km) and ash fall-out, the subsequent winnowing by bottom currents controlled the concentration of the volcanic grains previously disseminated inside the hemipelagic sediment. Palagonitisation, and especially phillipsite formation, may result from a relatively rapid reaction during burial diagenesis (<1 m.y.), in deep-sea deposits at relatively low sedimentation rate. However, it cannot be excluded that the weathering had begun widely on the Cameroon Ridge before the explosive event.

Isotopic and chemical compositions of rocks and minerals from the TAG hydrothermal mound, ODP Site 957

Strontium- and oxygen-isotopic measurements of samples recovered from the Trans-Atlantic Geotraverse (TAG) hydrothermal mound during Leg 158 of the Ocean Drilling Program provide important constraints on the nature of fluid-rock interactions during basalt alteration and mineralization within an active hydrothermal deposit. Fresh Mid-Ocean Ridge Basalt (MORB), with a 87Sr/86Sr of 0.7026, from the basement beneath the TAG mound was altered at both low and high temperatures by seawater and altered at high temperature by near end-member black smoker fluids. Pillow breccias occurring beneath the margins of the mound are locally recrystallized to chlorite by interaction with large volumes of conductively heated seawater (>200°C). The development of a silicified, sulfide-mineralized stockwork within the basaltic basement follows a simple paragenetic sequence of chloritization followed by mineralization and the development of a quartz+pyrite+paragonite stockwork cut by quartz-pyrite veins. Initial alteration involved the development of chloritic alteration halos around basalt clasts by reaction with a Mg-bearing mixture of upwelling, high-temperature (>300°C), black smoker-type fluid with a minor (<10%) proportion of seawater. Continued high-temperature (>300°C) interaction between the wallrock and these Mg-bearing fluids results in the complete recrystallization of the wallrock to chlorite+quartz+pyrite. The quartz+pyrite+paragonite assemblage replaces the chloritized basalts, and developed by reaction at 250-360°C with end-member hydrothermal fluids having 87Sr/86Sr ~0.7038, similar to present-day vent fluids. The uniformity of the 87Sr/86Sr ratios of hydrothermal assemblages throughout the mound and stockwork requires that the 87Sr/86Sr ratio of end-member hydrothermal fluids has remained relatively constant for a time period longer than that required to change the interior thermal structure and plumbing network of the mound and underlying stockwork. Precipitation of anhydrite in breccias and as late-stage veins throughout most of the mound and stockwork, down to at least 125 mbsf, records extensive entrainment of seawater into the hydrothermal deposit. 87Sr/86Sr ratios indicate that most of the anhydrite formed from ~2:1 mixture of seawater and black smoker fluids (65%±15% seawater). Oxygen-isotopic compositions imply that anhydrite precipitated at temperatures between 147°C and 270°C and require that seawater was conductively heated to between 100°C and 180°C before mixing and precipitation occurred. Anhydrite from the TAG mound has a Sr-Ca partition coefficient Kd ~0.60±0.28 (2 sigma). This value is in agreement with the range of experimentally determined partition coefficients (Kd ~0.27-0.73) and is similar to those calculated for anhydrite from active black smoker chimneys from 21°N on the East Pacific Rise. The d18O (for SO4) of TAG anhydrite brackets the value of seawater sulfate oxygen (~9.5?). Dissolution of anhydrite back into the oceans during episodes of hydrothermal quiescence provides a mechanism of buffering seawater sulfate oxygen to an isotopically light composition, in addition to the precipitation and dissolution of anhydrite within the oceanic basement during hydrothermal recharge at the mid-ocean ridges.

Isotopic composition of igneous rocks from DSDP Site 462

The tholeiitic basalts and microdolerites that comprise the Cretaceous igneous complex in the Nauru Basin in the western equatorial Pacific have moderate ranges in initial 87Sr/86Sr (0.70347 - 0.70356), initial 143Nd/144Nd (0.51278 - 0.51287), and measured 206Pb/204Pb (18.52 - 19.15), 207Pb/204Pb (15.48 - 15.66) and 208Pb/204Pb (38.28 - 38.81). These isotopic ratios overlap with those of both oceanic island basalts (OIB) and South Atlantic and Indian mid-ocean ridge basalts (MORB). However, the petrography, mineralogy, and bulk rock chemistry of the igneous complex are more similar to MORB than to OIB. Also, the rare earth element contents of Nauru Basin igneous rocks are uniformly depleted in light elements (La/Sm(ch) < 1) indicative of a mantle source compositionally similar to that of MORB. These results suggest that the igneous complex is the top of the original ocean crust in the Nauru Basin, and that the notion that the crust must be 15 to 35 m.y. older based on simple extrapolation and identification of the M-sequence magnetic lineations (Larson et al., 1981, doi:10.2973/dsdp.proc.61.1981; Moberly et al., 1985, doi:10.2973/dsdp.proc.81.1984) may be invalid because of a more complicated tectonic setting. The igneous complex most probably was extruded from an ocean ridge system located near the anomalously hot, volcanically active, and isotopically distinct region in the south central Pacific which has been in existence since c. 120 Ma.