Organic geochemistry of sediments from North Alex Mud Vulcano

Hydrocarbon seeps are ubiquitous at gas-prone Cenozoic deltas such as the Nile Deep Sea Fan (NDSF) where seepage into the bottom water has been observed at several mud volcanoes (MVs) including North Alex MV (NAMV). Here we investigated the sources of hydrocarbon gases and sedimentary organic matter together with biomarkers of microbial activity at four locations of NAMV to constrain how venting at the seafloor relates to the generation of hydrocarbon gases in deeper sediments. At the centre, high upward flux of hot (70 °C) hydrocarbon-rich fluids is indicated by an absence of biomarkers of Anaerobic Oxidation of Methane (AOM) and nearly constant methane (CH4) concentration depth-profile. The presence of lipids of incompatible thermal maturities points to mixing between early-mature petroleum and immature organic matter, indicating that shallow mud has been mobilized by the influx of deep-sourced hydrocarbon-rich fluids. Methane is enriched in the heavier isotopes, with values of d13C ~-46.6 per mil VPDB and dD ~-228 per mil VSMOW, and is associated with high amounts of heavier homologues (C2+) suggesting a co-genetic origin with the petroleum. On the contrary at the periphery, a lower but sustained CH4 flux is indicated by deeper sulphate-methane transition zones and the presence of 13C-depleted biomarkers of AOM, consistent with predominantly immature organic matter. Values of d13C-CH4 ~-60 per mil VPDB and decreased concentrations of 13C-enriched C2+ are typical of mixed microbial CH4 and biodegraded thermogenic gas from Plio-Pleistocene reservoirs of the region. The maturity of gas condensate migrated from pre-Miocene sources into Miocene reservoirs of the Western NDSF is higher than that of the gas vented at the centre of NAMV, supporting the hypothesis that it is rather released from the degradation of oil in Neogene reservoirs. Combined with the finding of hot pore water and petroleum at the centre, our results suggest that clay mineral dehydration of Neogene sediments, which takes place posterior to reservoir filling, may contribute to intense gas generation at high sedimentation rate deltas.

Geochemistry and mineralogy of ultramafic rocks from conical seamount

The Mariana arc-trench system, the easternmost of a series of backarc basins and intervening remnant arcs that form the eastern edge of the Philippine Sea Plate, is a well-known example of an intraoceanic convergence zone. Its evolution has been studied by numerous investigators over nearly two decades (e.g., Kang, 1971; Uyeda and Kanamori, 1979; LaTraille and Hussong, 1980; Fryer and Hussong, 1981; Mrosowski et al., 1982; Hussong and Uyeda, 1981; Bloomer and Hawkins, 1983; Karig and Ranken, 1983; McCabe and Uyeda, 1983; Hsui and Youngquist, 1985; Fryer and Fryer, 1987; Johnson and Fryer, 1988; Johnson and Fryer, 1989; Johnson et al., 1991). The Mariana forearc has undergone extensive vertical uplift and subsidence in response to seamount collision, to tensional and rotational fracturing associated with adjustments to plate subduction, and to changes in the configuration of the arc (Hussong and Uyeda, 1981; Fryer et al., 1985). Serpentine seamounts, up to 2500 m high and 30 km in diameter, occur in a broad zone along the outer-arc high (Fryer et al., 1985; Fryer and Fryer, 1987). These seamounts may be horsts of serpentinized ultramafic rocks or may have been formed by the extrusion of serpentine muds. Conical Seamount, one of these serpentine seamounts, is located within this broad zone of forearc seamounts, about 80 km from the trench axis, at about 19°30'N. The seamount is approximately 20 km in diameter and rises 1500 m above the surrounding seafloor. Alvin submersible, R/V Sonne bottom photography, seismic reflection, and SeaMARC II studies indicate that the surface of this seamount is composed of unconsolidated serpentine muds that contain clasts of serpentinized ultramafic and metamorphosed mafic rocks, and authigenic carbonate and silicate minerals (Saboda et al., 1987; Haggerty, 1987; Fryer et al., 1990; Saboda, 1991). During Leg 125, three sites were drilled (two flank sites and one summit site) on Conical Seamount to investigate the origin and evolution of the seamount. Site 778 (19°29.93'N, 146°39.94'E) is located in the midflank region of the southern quadrant of Conical Seamount at a depth of 3913.7 meters below sea level (mbsl) (Fig. 2). This site is located in the center of a major region of serpentine flows (Fryer et al., 1985, 1990). Site 779 (19°30.75'N, 146°41.75'E), about 3.5 km northeast of Site 778, is located approximately in the midflank region of the southeast quadrant of Conical Seamount, at a depth of 3947.2 mbsl. This area is mantled by a pelagic sediment cover, overlying exposures of unconsolidated serpentine muds that contain serpentinized clasts of mafic and ultramafic rocks (Fryer et al., 1985, 1990). Site 780 (19°32.5'N, 146°39.2'E) is located on the western side of Conical Seamount near the summit, at a depth of 3083.4 mbsl. This area is only partly sediment covered and lies near active venting fields where chimney structures are forming (Fryer et al., 1990).

Microbial community, biomarker concentrations and their isotopic signature in sediment of Gullfaks and Tommeliten methane seeps in the Northern North Sea

Gullfaks is one of the four major Norwegian oil and gas fields, located in the northeastern edge of the North Sea Plateau. Tommeliten lies in the greater Ekofisk area in the central North Sea. During the cruises HE 208 and AL 267 several seep locations of the North Sea were visited. At the Heincke seep at Gullfaks, sediments were sampled in May 2004 (HE 208) using a video-guided multiple corer system (MUC; Octopus, Kiel). The samples were recovered from an area densely covered with bacterial mats where gas ebullition was observed. The coarse sands limited MUC penetration depth to maximal 30 centimeters and the highly permeable sands did not allow for a high-resolution, vertical subsampling because of pore water loss. The gas flare mapping and videographic observation at Tommeliten indicated an area of gas emission with a few small patches of bacterial mats with diameters <50 cm from most of which a single stream of gas bubbles emerged. The patches were spaced apart by 10-100 m. Sampling of sediments covered by bacterial mats was only possible with 3 small push cores (3.8 cm diameter) mounted to ROV Cherokee. These cores were sampled in 3 cm intervals. Lipid biomarker extraction from 10 -17 g wet sediment was carried out as described in detail elsewhere (Elvert et al., 2003; doi:10.1080/01490450303894). Briefly, defined concentrations of cholestane, nonadecanol and nonadecanolic acid with known delta 13C-values were added to the sediments prior to extraction as internal standards for the hydrocarbon, alcohol and fatty acid fraction, respectively. Total lipid extracts were obtained from the sediment by ultrasonification with organic solvents of decreasing polarity. Esterified fatty acids (FAs) were cleaved from the glycerol head group by saponification with methanolic KOH solution. From this mixture, the neutral fraction was extracted with hexane. After subsequent acidification, FAs were extracted with hexane. For analysis, FAs were methylated using BF3 in methanol yielding fatty acid methyl esters (FAMES). The fixation for total cell counts and CARD-FISH were performed on-board directly after sampling. For both methods, sediments were fixed in formaldehyde solution. After two hours, aliquots for CARD-FISH staining were washed with 1* PBS (10mmol/l sodium phosphate solution, 130mmol/l NaCl, adjusted to a pH of 7.2) and finally stored in a 1:1 PBS:ethanol solution at -20°C until further processing. Samples for total cell counts were stored in formalin at 4°C until analysis. For sandy samples, the total cell count/CARD-FISH protocol was optimized to separate sand particles from the cells. Cells were dislodged from sediment grains and brought into solution with the supernatant by sonicating each sample onice for 2 minutes at 50W. This procedure was repeated four times and supernatants were combined. The sediment samples were brought to a final dilution of 1:2000 to 1:4000 and filtered onto 0.2µm GTTP filters (Millipore, Eschbonn, Germany).

Mineralogy of cold seep sediment inhabited by vesicomyid clams in the Japan Deep Sea Trench

Sediment sampling was performed at the center of the clam colony. Immediately after sample recovery onboard, the sediment core was sub-sampled and preserved for later analyses. Pyrite and carbonate content of the sediment was measured by X-ray refraction analysis as previously described (Ertefai et al., 2010).

Ex situ sulphate reduction rates of sediment at the rim of a vesicomyd clam colony in the Japan Deep Sea Trench (dive 955)

Sediment samples were collected from the rim of a large vesicomyid clam colony in the Japan Deep Sea Trench. Immediately after sample recovery onboard, the sediment core was sub-sampled for ex situ rate measurements. Sulfate reduction were measured ex situ by the whole core injection method with three replicates. We incubated the samples at in situ temperature (1.5°C) for 48 hours with carrier-free 35SO4 (dissolved in water, 50 kBq). Sediment was fixed 20 ml ZnAc solution (20%, w/v) for AOM or SR. Turnover rates were measured as previously described (Kallmeyer et al., 2004).

Employment rate impacts of charging the Heavy Good Vehicle corridor (Madrid-Sevilla) across Spanish regions: a Random Utility Based Multiregional Input-Output approach

The implementation of a charging policy for heavy goods vehicles in European Union (EU) member countries has been imposed to reflect costs of construction and maintenance of infrastructure as well as externalities such as congestion, accidents and environmental impact. In this context, EU countries approved the Eurovignette directive (1999/62/EC) and its amending directive (2006 /38/EC) which established a legal framework to regulate the system of tolls. Even if that regulation seek s to increase the efficien cy of freight, it will trigger direct and indirect effects on Spain’s regional economies by increasing transport costs. This paper presents the development of a multiregional Input-Output methodology (MRIO) with elastic trade coefficients to predict in terregional trade, using transport attributes integrated in multinomial logit models. This method is highly useful to carry out an ex-ante evaluation of transport policies because it involves road freight transport cost sensitivity, and determine regional distributive and substitution economic effect s of countries like Spain, characterized by socio-demographic and economic attributes, differentiated region by region. It will thus be possible to determine cost-effective strategies, given different policy scenarios. MRIO mode l would then be used to determine the impact on the employment rate of imposing a charge in the Madrid-Sevilla corridor in Spain. This methodology is important for measuring the impact on the employment rate since it is one of the main macroeconomic indicators of Spain’s regional and national economic situation. A previous research developed (DESTINO) using a MRIO method estimated employment impacts of road pricing policy across Spanish regions considering a fuel tax charge (€/liter) in the entire shortest cost path network for freight transport. Actually, it found that the variation in employment is expected to be substantial for some regions, and negligible for others. For example, in this Spanish case study of regional employment has showed reductions between 16.1% (Rioja) and 1.4% (Madrid region). This variation range seems to be related to either the intensity of freight transport in each region or dependency of regions to transport intensive economic sect ors. In fact, regions with freight transport intensive sectors will lose more jobs while regions with a predominantly service economy undergo a fairly insignificant loss of employment. This paper is focused on evaluating a freight transport vehicle-kilometer charge (€/km) in a non-tolled motorway corridor (A-4) between Madrid-Sevilla (517 Km.). The consequences of the road pricing policy implementation show s that the employment reductions are not as high as the diminution stated in the previous research because this corridor does not affect the whole freight transport system of Spain.

Development of a Knowledge Base for smart screening of language disorders in primary care

Monitoring of neuro-evolutive development from birth until the age of six is a decisive factor in a child's quality of life. Early detection of development disorders in early childhood can facilitate necessary diagnosis and/or treatment. Primary-care pediatricians play a key role in early detection of development alterations as they can undertake the preventive and therapeutic actions necessary in the interest of a child's optimal development. The focus of this research paper is the construction of a Knowledge Base for smart screening aimed to assist pediatricians in processes of early referral in language disorders. The proposed model provides health professionals with a decision-making tool that supports referral processes. In this way, essential diagnostic and/or therapeutic actions are triggered for a comprehensive individual development. The resulting system was developed on the basis of an analysis and verification of 21 cases of children with language disorders.

Hysteresis in transverse galloping: the role of the inflection points

Transverse galloping is here considered as a one-degree-of-freedom oscillator subjected to aerodynamic forces, which are described by using the quasi-steady hypothesis. The hysteresis of transverse galloping is also analyzed. Approximate solutions of the model are obtained by assuming that the aerodynamic and damping forces are much smaller than the inertial and stiffness ones. The analysis of the approximate solution, which is obtained by means of the method of Krylov–Bogoliubov, reveals the existing link between the hysteresis phenomenon and the number of inflection points at the aerodynamic force coefficient curve, Cy(α)Cy(α); CyCy and αα being, respectively, the force coefficient normal to the incident flow and the angle of attack. The influence of the position of these inflection points on the range of flow velocities in which hysteresis takes place is also analyzed.

Typing of urinary JC virus DNA offers a novel means of tracing human migrations

Although polyomavirus JC (JCV) is the proven pathogen of progressive multifocal leukoencephalopathy, the fatal demyelinating disease, this virus is ubiquitous as a usually harmless symbiote among human beings. JCV propagates in the adult kidney and excretes its progeny in urine, from which JCV DNA can readily be recovered. The main mode of transmission of JCV is from parents to children through long cohabitation. In this study, we collected a substantial number of urine samples from native inhabitants of 34 countries in Europe, Africa, and Asia. A 610-bp segment of JCV DNA was amplified from each urine sample, and its DNA sequence was determined. A worldwide phylogenetic tree subsequently constructed revealed the presence of nine subtypes including minor ones. Five subtypes (EU, Af2, B1, SC, and CY) occupied rather large territories that overlapped with each other at their boundaries. The entire Europe, northern Africa, and western Asia were the domain of EU, whereas the domain of Af2 included nearly all of Africa and southwestern Asia all the way to the northeastern edge of India. Partially overlapping domains in Asia were occupied by subtypes B1, SC, and CY. Of particular interest was the recovery of JCV subtypes in a pocket or pockets that were separated by great geographic distances from the main domains of those subtypes. Certain of these pockets can readily be explained by recent migrations of human populations carrying these subtypes. Overall, it appears that JCV genotyping promises to reveal previously unknown human migration routes: ancient as well as recent.

Characterization of the α1B-adrenergic receptor gene promoter region and hypoxia regulatory elements in vascular smooth muscle

We previously demonstrated that α1B-adrenergic receptor (AR) gene transcription, mRNA, and functionally coupled receptors increase during 3% O2 exposure in aorta, but not in vena cava smooth muscle cells (SMC). We report here that α1BAR mRNA also increases during hypoxia in liver and lung, but not heart and kidney. A single 2.7-kb α1BAR mRNA was detected in aorta and vena cava during normoxia and hypoxia. The α1BAR 5′ flanking region was sequenced to −2,460 (relative to ATG +1). Transient transfection experiments identify the minimal promoter region between −270 and −143 and sequence between −270 and −248 that are required for transcription of the α1BAR gene in aorta and vena cava SMC during normoxia and hypoxia. An ATTAAA motif within this sequence specifically binds aorta, vena cava, and DDT1MF-2 nuclear proteins, and transcription primarily initiates downstream of this motif at approximately −160 in aorta SMC. Sequence between −837 and −273 conferred strong hypoxic induction of transcription in aorta, but not in vena cava SMC, whereas the cis-element for the transcription factor, hypoxia-inducible factor 1, conferred hypoxia-induced transcription in both aorta and vena cava SMC. These data identify sequence required for transcription of the α1BAR gene in vascular SMC and suggest the atypical TATA-box, ATTAAA, may mediate this transcription. Hypoxia-sensitive regions of the α1BAR gene also were identified that may confer the differential hypoxic increase in α1BAR gene transcription in aorta, but not in vena cava SMC.

The N-terminal 209-aa domain of high molecular- weight 4.1R isoforms abrogates 4.1R targeting to the nucleus

An extensive repertoire of protein 4.1R isoforms is predominantly generated by alternative pre-mRNA splicing and differential usage of two translation initiation sites. The usage of the most upstream ATG (ATG-1) generates isoforms containing N-terminal extensions of up to 209 aa compared with those translated from the downstream ATG (ATG-2). To characterize nonerythroid 4.1R proteins translated from ATG-1 and analyze their intracellular localization, we cloned 4.1R cDNAs containing this translation initiation site. Six different clones were isolated from the nucleated human MOLT-4 T-cell line by reverse transcriptase–PCR techniques. Transient expression of the six ATG-1-translated 4.1R isoforms tagged with a c-Myc epitope revealed that all of them predominantly distributed to the plasma membrane and the endoplasmic reticulum. Staining of MOLT-4 cell plasma membranes but not nuclei was also observed by immunofluorescence microscopy by using an antibody specific to the N-terminal extension. Consistent with this, the antibody reacted with a major endogenous protein of ≈145 kDa present in nonnuclear but absent from nuclear fractions prepared from MOLT-4 cells. Because these data suggested that ATG-1-translated 4.1R isoforms were predominantly excluded from the nucleus, we fused the 209-aa domain to nuclear 4.1R isoforms encoded from ATG-2 and observed that this domain inhibited their nuclear targeting. All these results indicate that the N-terminal domain of ATG-1-translated 4.1R isoforms plays a pivotal role in differential targeting of proteins 4.1R.

The Crithidia fasciculata RNH1 gene encodes both nuclear and mitochondrial isoforms of RNase H

The Crithidia fasciculata RNH1 gene encodes an RNase H, an enzyme that specifically degrades the RNA strand of RNA–DNA hybrids. The RNH1 gene is contained within an open reading frame (ORF) predicted to encode a protein of 53.7 kDa. Previous work has shown that RNH1 expresses two proteins: a 38 kDa protein and a 45 kDa protein which is enriched in kinetoplast extracts. Epitope tagging of the C-terminus of the RNH1 gene results in localization of the protein to both the kinetoplast and the nucleus. Translation of the ORF beginning at the second in-frame methionine codon predicts a protein of 38 kDa. Insertion of two tandem stop codons between the first ATG codon and the second in-frame ATG codon of the ORF results in expression of only the 38 kDa protein and the protein localizes specifically to the nucleus. Mutation of the second methionine codon to a valine codon prevents expression of the 38 kDa protein and results in exclusive production of the 45 kDa protein and localization of the protein only in the kinetoplast. These results suggest that the kinetoplast enzyme results from processing of the full-length 53.7 kDa protein. The nuclear enzyme appears to result from translation initiation at the second in-frame ATG codon. This is the first example in trypanosomatids of the production of nuclear and mitochondrial isoforms of a protein from a single gene and is the only eukaryotic gene in the RNase HI gene family shown to encode a mitochondrial RNase H.