Geochemistry and isotopic composition of gabbros from ODP Hole 118-375B

Gabbros drilled from the shallow (720 m) east wall of the Atlantis II transform on the Southwest Indian Ridge (SWIR; 32°43.40', 57°16.00') provide the most complete record of the stratigraphy and composition of the oceanic lower crust recovered from the ocean basins to date. Lithologies recovered include gabbro, olivine gabbro, troctolite, trondhjemite, and unusual iron-titanium (FeTi) oxide-rich gabbro containing up to 30% FeTi oxides. The plutonic rock sequence represents a tholeiitic fractionation trend ranging from primitive magmas having Mg numbers of 67 to 69 that fractionated troctolites, to highly evolved liquids that crystallized two-pyroxene, FeTi oxide-rich gabbros and, ultimately, trondhjemite. Isotopic compositions of unaltered Leg 118 gabbros are distinct from Indian Ocean mid-ocean ridge basalts (MORB) in having higher 143Nd/144Nd (0.51301-0.51319) and lower 206Pb/204Pb values (17.35-17.67); 87Sr/86Sr values (0.7025-0.7030) overlap those of SWIR basalts, but are generally lower than MORBs from the Southeast Indian Ridge or the Rodrigues Triple Junction. More than one magma composition may have been introduced into the magma chamber during its crystallization history, as suggested by the higher 87Sr/86Sr, 206Pb/204Pb, and lower 143Nd/144Nd values of chromium-rich olivine gabbros from the bottom of Hole 735B. Whole-rock gabbro and plagioclase mineral separate 87Sr/86Sr values are uniformly low (0.7027-0.7030), irrespective of alteration and deformation. By contrast, 87Sr/86Sr values for clinopyroxene (0.7025-0.7039) in the upper half of Hole 735B are higher than coexisting plagioclase and reflect extensive replacement of clinopyroxene by amphibole. Hydrothermal veins and breccias have elevated 87Sr/86Sr values (0.7029-0.7035) and indicate enhanced local introduction of seawater strontium. Oxygen- and hydrogen-isotope results show that secondary amphiboles have uniform dD values of -49 to -54 per mil and felsic hydrothermal veins range from -46 to - 77 per mil. Oxygen-isotope data for secondary amphibole and visibly altered gabbros range to low values (+1.0-+5.5 per mil), and O-isotope disequilibrium between coexisting pyroxene and plagioclase pairs from throughout the stratigraphic column indicates that seawater interacted with much of the gabbro section, but at relatively low water/rock ratios. This is consistent with the persistence of low 87Sr/86Sr values, even in gabbros that were extensively deformed and altered.

(Table T1) Mineral composition of turbidite sands and sandstones from ODP Leg 190 sites

During Ocean Drilling Program Leg 190 several turbidite successions in the Nankai Trough were drilled through including Pleistocene trench fill (Sites 1173 and 1174), Pleistocene-Pliocene slope basin deposits and underlying trench fill (Sites 1175 and 1176), Miocene Shikoku Basin deposits (Site 1177), and upper Miocene trench fill (Site 1178). Sands from the Pleistocene trench-fill succession of the Nankai Trough are of mixed derivation with significant monomineralic components (quartz and feldspar) and mafic to intermediate volcanic rock fragments, in addition to sedimentary and less abundant metamorphic detritus. They have a source in the Izu collision zone in central Honshu. Sands from the slope and accreted trench fill at Sites 1175 and 1176 are dominated by quartz with less abundant feldspar, sedimentary rock fragments, and only minor volcanic and metamorphic rock fragments. In contrast to the trench turbidites of Sites 1173 and 1174, these sands are very quartzose with characteristic radiolarian chert fragments. Volcanic rock fragments are mainly of silicic composition. Potential sources of these sands are uplifted subduction complexes of southwest Japan. Sands from the accreted trench turbidites at Site 1178 have clast types similar to those at Sites 1175 and 1176. In contrast, however, framework detrital modes are distinctive, with Site 1178 sands having substantially lower total quartz contents and more abundant fine-grained sedimentary rock fragments. These sands were also probably derived from the island of Shikoku, but their composition indicates that sedimentary rocks were abundant in the source area and these may have been Miocene forearc basin successions that were largely removed by erosion. Erosional remnants of Miocene forearc basin deposits are present on the Kii Peninsula east-northeast of Shikoku. Erosion followed a phase of exhumation of the Shimanto Belt indicated by apatite fission track ages at ~10 Ma. Sand in the lower-upper Miocene turbidites of the lower Shikoku Basin section at Site 1177 is more varied in composition, with the upper part of the unit similar to Site 1178 (i.e., rich in sedimentary rock fragments) and the lower part similar to those at Sites 1175 and 1176 (i.e., rich in quartz with some silicic volcanic rock fragments). Sands from the lower part of the Miocene turbidite unit were derived from a continental source with plutonic and volcanic rocks, possibly the inner zone of southwest Japan.

Oxygen and sulfur isotopes of peridotite and gabbro from the Mid-Atlantic Ridge

Whole rock sulfur and oxygen isotope compositions of altered peridotites and gabbros from near the 15°20'N Fracture Zone on the Mid-Atlantic Ridge were analyzed to investigate hydrothermal alteration processes and test for a subsurface biosphere in oceanic basement. Three processes are identified. (1) High-temperature hydrothermal alteration (~250-350°C) at Sites 1268 and 1271 is characterized by 18O depletion (2.6-4.4 per mil), elevated sulfide-S, and high delta34S (up to ~2 wt% and 4.4-10.8 per mil). Fluids were derived from high-temperature (>350°C) reaction of seawater with gabbro at depth. These cores contain gabbroic rocks, suggesting that associated heat may influence serpentinization. (2) Low-temperature (<150°C) serpentinization at Sites 1272 and 1274 is characterized by elevated delta18O (up to 8.1 per mil), high sulfide-S (up to ~3000 ppm), and negative delta34S (to -32.1 per mil) that reflect microbial reduction of seawater sulfate. These holes penetrate faults at depth, suggesting links between faulting and temperatures of serpentinization. (3) Late low-temperature oxidation of sulfide minerals caused loss of sulfur from rocks close to the seafloor. Sulfate at all sites contains a component of oxidized sulfide minerals. Low delta34S of sulfate may result from kinetic isotope fractionation during oxidation or may indicate readily oxidized low-delta34S sulfide derived from microbial sulfate reduction. Results show that peridotite alteration may be commonly affected by fluids +/- heat derived from mafic intrusions and that microbial sulfate reduction is widespread in mantle exposed at the seafloor.

A Retrospective View of Software Maintenance and Reengineering Research.

As a summary of past, current, and future trends in software maintenance and reengineering research, we give in this editorial a retrospective look from the past 14 years to now. We provide insight on how software maintenance has evolved and on the most important research topics presented in the series of the European Conference on Software Maintenance and Reengineering.

Finite element code-based modeling of a multi-feature isolation system and passive alleviation of possible inner pounding

The existing seismic isolation systems are based on well-known and accepted physical principles, but they are still having some functional drawbacks. As an attempt of improvement, the Roll-N-Cage (RNC) isolator has been recently proposed. It is designed to achieve a balance in controlling isolator displacement demands and structural accelerations. It provides in a single unit all the necessary functions of vertical rigid support, horizontal flexibility with enhanced stability, resistance to low service loads and minor vibration, and hysteretic energy dissipation characteristics. It is characterized by two unique features that are a self-braking (buffer) and a self-recentering mechanism. This paper presents an advanced representation of the main and unique features of the RNC isolator using an available finite element code called SAP2000. The validity of the obtained SAP2000 model is then checked using experimental, numerical and analytical results. Then, the paper investigates the merits and demerits of activating the built-in buffer mechanism on both structural pounding mitigation and isolation efficiency. The paper addresses the problem of passive alleviation of possible inner pounding within the RNC isolator, which may arise due to the activation of its self-braking mechanism under sever excitations such as near-fault earthquakes. The results show that the obtained finite element code-based model can closely match and accurately predict the overall behavior of the RNC isolator with effectively small errors. Moreover, the inherent buffer mechanism of the RNC isolator could mitigate or even eliminate direct structure-tostructure pounding under severe excitation considering limited septation gaps between adjacent structures. In addition, the increase of inherent hysteretic damping of the RNC isolator can efficiently limit its peak displacement together with the severity of the possibly developed inner pounding and, therefore, alleviate or even eliminate the possibly arising negative effects of the buffer mechanism on the overall RNC-isolated structural responses.

Xeroderma pigmentosum and trichothiodystrophy are associated with different mutations in the XPD (ERCC2) repair/transcription gene

The xeroderma pigmentosum group D (XPD) protein has a dual function, both in nucleotide excision repair of DNA damage and in basal transcription. Mutations in the XPD gene can result in three distinct clinical phenotypes, XP, trichothiodystrophy (TTD), and XP with Cockayne syndrome. To determine if the clinical phenotypes of XP and TTD can be attributed to the sites of the mutations, we have identified the mutations in a large group of TTD and XP-D patients. Most sites of mutations differed between XP and TTD, but there are three sites at which the same mutation is found in XP and TTD patients. Since the corresponding patients were all compound heterozygotes with different mutations in the two alleles, the alleles were tested separately in a yeast complementation assay. The mutations which are found in both XP and TTD patients behaved as null alleles, suggesting that the disease phenotype was determined by the other allele. If we eliminate the null mutations, the remaining mutagenic pattern is consistent with the site of the mutation determining the phenotype.

Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination

When gene conversion is initiated by a double-strand break (DSB), any nonhomologous DNA that may be present at the ends must be removed before new DNA synthesis can be initiated. In Saccharomyces cerevisiae, removal of nonhomologous ends depends not only on the nucleotide excision repair endonuclease Rad1/Rad10 but also on Msh2 and Msh3, two proteins that are required to correct mismatched bp. These proteins have no effect when DSB ends are homologous to the donor, either in the kinetics of recombination or in the proportion of gene conversions associated with crossing-over. A second DSB repair pathway, single-strand annealing also requires Rad1/Rad10 and Msh2/Msh3, but reveals a difference in their roles. When the flanking homologous regions that anneal are 205 bp, the requirement for Msh2/Msh3 is as great as for Rad1/Rad10; but when the annealing partners are 1,170 bp, Msh2/Msh3 have little effect, while Rad1/Rad10 are still required. Mismatch repair proteins Msh6, Pms1, and Mlh1 are not required. We suggest Msh2 and Msh3 recognize not only heteroduplex loops and mismatched bp, but also branched DNA structures with a free 3′ tail.

Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain

The Escherichia coli DNA repair enzyme MutY plays an important role in the prevention of DNA mutations by removing misincorporated adenine residues from 7,8-dihydro-8-oxo-2′-deoxyguanosine:2′-deoxyadenosine (OG:A) mispairs. The N-terminal domain of MutY (Stop 225, Met1–Lys225) has a sequence and structure that is characteristic of a superfamily of base excision repair glycosylases; however, MutY and its homologs contain a unique C-terminal domain. Previous studies have shown that the C-terminal domain confers specificity for OG:A substrates over G:A substrates and exhibits homology to the d(OG)TPase MutT, suggesting a role in OG recognition. In order to provide additional information on the importance of the C-terminal domain in damage recognition, we have investigated the kinetic properties of a form lacking this domain (Stop 225) under multiple- and single-turnover conditions. In addition, the interaction of Stop 225 with a series of non-cleavable substrate and product analogs was evaluated using gel retardation assays and footprinting experiments. Under multiple-turnover conditions Stop 225 exhibits biphasic kinetic behavior with both OG:A and G:A substrates, likely due to rate-limiting DNA product release. However, the rate of turnover of Stop 225 was increased 2-fold with OG:A substrates compared to the wild-type enzyme. In contrast, the intrinsic rate for adenine removal by Stop 225 from both G:A and OG:A substrates is significantly reduced (10- to 25-fold) compared to the wild-type. The affinity of Stop 225 for substrate analogs was dramatically reduced, as was the ability to discriminate between substrate analogs paired with OG over G. Interestingly, similar hydroxyl radical and DMS footprinting patterns are observed for Stop 225 and wild-type MutY bound to DNA duplexes containing OG opposite an abasic site mimic or a non-hydrogen bonding A analog, suggesting that similar regions of the DNA are contacted by both enzyme forms. Importantly, Stop 225 has a reduced ability to prevent DNA mutations in vivo. This implies that the reduced adenine glycosylase activity translates to a reduced capacity of Stop 225 to prevent DNA mutations in vivo.

The Polo-like Kinase Plx1 Is Required for Activation of the Phosphatase Cdc25C and Cyclin B-Cdc2 in Xenopus Oocytes

In the Xenopus oocyte system mitogen treatment triggers the G2/M transition by transiently inhibiting the cAMP-dependent protein kinase (PKA); subsequently, other signal transduction pathways are activated, including the mitogen-activated protein kinase (MAPK) and polo-like kinase pathways. To study the interactions between these pathways, we have utilized a cell-free oocyte extract that carries out the signaling events of oocyte maturation after addition of the heat-stable inhibitor of PKA, PKI. PKI stimulated the synthesis of Mos and activation of both the MAPK pathway and the Plx1/Cdc25C/cyclin B-Cdc2 pathway. Activation of the MAPK pathway alone by glutathione S-transferase (GST)-Mos did not lead to activation of Plx1 or cyclin B-Cdc2. Inhibition of the MAPK pathway in the extract by the MEK1 inhibitor U0126 delayed, but did not prevent, activation of the Plx1 pathway, and inhibition of Mos synthesis by cycloheximide had a similar effect, suggesting that MAPK activation is the only relevant function of Mos. Immunodepletion of Plx1 completely inhibited activation of Cdc25C and cyclin B-Cdc2 by PKI, indicating that Plx1 is necessary for Cdc25C activation. In extracts containing fully activated Plx1 and Cdc25C, inhibition of cyclin B-Cdc2 by p21Cip1 had no significant effect on either the phosphorylation of Cdc25C or the activity of Plx1. These results demonstrate that maintenance of Plx1 and Cdc25C activity during mitosis does not require cyclin B-Cdc2 activity.

Mutagenesis by third-strand-directed psoralen adducts in repair-deficient human cells: high frequency and altered spectrum in a xeroderma pigmentosum variant.

Psoralen-conjugated triple-helix-forming oligonucleotides have been used to generate site-specific mutations within mammalian cells. To investigate factors influencing the efficiency of oligonucleotide-mediated gene targeting, the processing of third-strand-directed psoralen adducts was compared in normal and repair-deficient human cells. An unusually high mutation frequency and an altered mutation pattern were seen in xeroderma pigmentosum variant (XPV) cells compared with normal, xeroderma pigmentosum group A (XPA), and Fanconi anemia cells. In XPV, targeted mutations were produced in the supF reporter gene carried in a simian virus 40 vector at a frequency of 30%, 3-fold above that in normal or Fanconi anemia cells and 6-fold above that in XPA. The mutations generated by targeted psoralen crosslinks and monoadducts in the XPV cells formed a pattern distinct from that in the other three cell lines, with mutations occurring not just at the damaged site but also at adjacent base pairs. Hence, the XPV cells may have an abnormality in trans-lesion bypass synthesis during repair and/or replication, implicating a DNA polymerase or an accessory factor as a basis of the defect in XPV. These results may help to elucidate the repair deficiency in XPV, and they raise the possibility that genetic manipulation via triplex-targeted mutagenesis may be enhanced by modulation of the XPV-associated activity in normal cells.

Coenzyme Q reductase from liver plasma membrane: purification and role in trans-plasma-membrane electron transport.

A specific requirement for coenzyme Q in the maintenance of trans-plasma-membrane redox activity is demonstrated. Extraction of coenzyme Q from membranes resulted in inhibition of NADH-ascorbate free radical reductase (trans electron transport), and addition of coenzyme Q10 restored the activity. NADH-cytochrome c oxidoreductase (cis electron transport) did not respond to the coenzyme Q status. Quinone analogs inhibited trans-plasma-membrane redox activity, and the inhibition was reversed by coenzyme Q. A 34-kDa coenzyme Q reductase (p34) has been purified from pig-liver plasma membranes. The isolated enzyme was sensitive to quinone-site inhibitors. p34 catalyzed the NADH-dependent reduction of coenzyme Q10 after reconstitution in phospholipid liposomes. When plasma membranes were supplemented with extra p34, NADH-ascorbate free radical reductase was activated but NADH-cytochrome c oxidoreductase was not. These results support the involvement of p34 as a source of electrons for the trans-plasma-membrane redox system oxidizing NADH and support coenzyme Q as an intermediate electron carrier between NADH and the external acceptor ascorbate free radical.

CC-1065 and the duocarmycins: unraveling the keys to a new class of naturally derived DNA alkylating agents.

Key studies defining the DNA alkylation properties and selectivity of a new class of exceptionally potent, naturally occurring antitumor antibiotics including CC-1065, duocarmycin A, and duocarmycin SA are reviewed. Recent studies conducted with synthetic agents containing deep-seated structural changes and the unnatural enantiomers of the natural products and related analogs have defined the structural basis for the sequence-selective alkylation of duplex DNA and fundamental relationships between chemical structure, functional reactivity, and biological properties. The agents undergo a reversible, stereoelectronically controlled adenine-N3 addition to the least substituted carbon of the activated cyclopropane within selected AT-rich sites. The preferential AT-rich non-covalent binding selectivity of the agents within the narrower, deeper AT-rich minor groove and the steric accessibility to the alkylation site that accompanies deep AT-rich minor groove penetration control the sequence-selective DNA alkylation reaction and stabilize the resulting adduct. For the agents that possess sufficient reactivity to alkylate DNA, a direct relationship between chemical or functional stability and biological potency has been defined.