Identification of genetic variants that influence atherosclerosis in young persons

Atherosclerosis is widely accepted as a complex genetic phenotype and is the usual cause of cardiovascular disease, the world’s leading killer. Genetic factors have been proven to be important risk contributors for atherosclerosis and much work has been done to identify promising candidates that might play a role in the development of atherosclerosis. It is well known that many independent replications are needed to unequivocally establish a valid genotype-phenotype association across different populations before the findings are extended to clinical settings and to the expensive follow-up studies designed to identify causal genetic variants. Aiming to replicate the association with atherosclerosis in the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study, we assessed the relationship of 32 atherosclerosis candidate SNPs to atherosclerosis in the PDAY cohort, consisting of AA and EA young people aged 15-34 years who died of non-medical causes. Two association studies, a whole sample study and a 1:1 matched case control study were performed by use of multiple linear regression and logistic regression analyses, respectively. For the whole sample association study, 32 SNPs among 2,650 individuals (1,369 AA and 1,281 EA) were tested for the association with six early atherosclerosis phenotypes: abdominal aorta fatty streaks, abdominal aorta raised lesions, right coronary artery fatty streaks, right coronary artery raised lesions, thoracic aorta fatty streaks, and thoracic aorta raised lesions. For the matched case-control association study, 337 case-control paired samples were included; cases were chosen with the highest total raised lesion scores from the studied population, while controls were randomly selected from individuals that had no raised lesions and matched to cases by age, gender and race. Sixteen SNPs in 13 genes were found to be significantly associated with atherosclerosis in at least one of the PDAY association studies. Among these 16 findings: eight SNPs (rs9579646, rs6053733, rs3849150, rs10499903, rs2148079, rs5073691, rs10116277, and rs17228212) successfully replicated previous results, six SNPs (rs17222814, rs10811661, rs7028570, rs7291467, rs16996148 and rs10401969) were reported as new findings exclusive to our study, the last two of the 16 SNPs, rs501120 and rs6922269, showed either intriguing or conflicting result. SNP rs17222814 in ALOX5AP and SNP rs3849150 in LRRC18 were consistently associated with atherosclerosis in both prior and the two PDAY association studies. SNP rs3849150 was also identified to be highly correlated with a non-synonymous coding SNP, rs17772611, which may damage the protein (polyphen score = 0.996), suggesting that SNP rs17772611 may be the causal functional variant.^ In conclusion, our study added more support for the association of these candidate genes with atherosclerosis. SNPs rs3849150 and rs17772611 of LRRC18, as well as SNP rs17222814 of ALOX5AP, were the most significant findings from our study, and may be ranked among the best for further study.^

Dinoflagellate cyst counts and age model from sediment samples of ODP Hole 175-1085A

Sediment samples from ODP Site 1085 were investigated in order to obtain more information on the initiation and development of the Benguela upwelling system during the middle and upper Miocene. In particular, our intent was to establish the causes of the upwelling as well as the response of the upwelling regime to the development of the Antarctic Circumpolar Current. Based on changes in the calcareous dinoflagellate cyst association, we found an initial increase of the dinoflagellate cyst productivity, probably related to the initiation of upwelling about 11.8 Ma ago. Two distinct increases in cyst productivity in conjunction with temperature decreases of the upper water masses reflect upwelling pulses off Namibia and occur at the end of the Miocene cooling events Mi5 (about 11.5 Ma) and Mi6 (about 10.5 Ma). Both cooling events are associated with an ice volume increase in Antarctica and are thought to have led to an increase in southeasterly winds, possibly causing these two upwelling pulses. We demonstrate a decrease in dinoflagellate cyst productivity and enhanced terrigenous input via the Orange River after the Mi5 event. At about 11.1 Ma, the dinoflagellate cyst productivity increases again. The polar cyst species Caracomia arctica occurs here for the first time. This implies an influence of subantarctic mode water and therefore a change in the quality of the upwelling water which allowed the Benguela upwelling to develop into modern conditions. From about 10.4 Ma, C. arctica forms a permanent part of the association, pointing to an establishment of the upwelling regime.

Geochemical studies of surface sediment samples off North-West Africa

One hundred and twenty-eight surface-sediment samples collected off North-West Africa were studied geochemically to detect the expressions of different meridional climate regimes and zonal productivity gradients in the surface sediments. This geochemical multi-tracer approach, coupled with additional information on the bulk carbonate and TOC contents makes it possible to characterise the sedimentological regime in detail. Typical terrigenous elements like Al, K and Fe mirror the importance of the humid (fluvial) influence in the north of the study area and the dominance of aeolian input in the south. Furthermore, the distributions of Ti and Fe in the surface sediments serve as tracers for the supply of eolian volcanic material from the Canary Islands. The spatial variability of the TOC contents in the surface sediments closely follows the ocean surface productivity patterns, whereas the CaCO3 contents are mainly controlled by dilution with terrigenous matter. The potential productivity proxy Ba is not a reliable tracer for productivity in this region, since it is mainly supplied by terrigenous input (coupled with aluminosilicates).

Radionuclides measured on water bottle samples during SONNE cruise SO202 (INOPEX)

Boundary scavenging, or the enhanced removal of adsorption-prone elements from the ocean in areas of high particle flux, is an often cited, though not well-quantified, concept used to understand the oceanic distribution of many trace metals. Because 230Th and 231Pa are produced uniformly from uranium decay and removed differentially by scavenging, the process of boundary scavenging can be elucidated by a more detailed knowledge of their water column distributions. To this end, filtered seawater was collected across the gradients in particle flux which span the subarctic Pacific: in the west during the Innovative North Pacific Experiment (INOPEX) and in the east along Line P. Lateral concentration gradients of dissolved 230Th are small throughout the subarctic Pacific at 12 sites of variable particle flux. This contradicts the prediction of the traditional boundary scavenging model. A compilation of water column data from throughout the North Pacific reveals much larger lateral concentration gradients for 230Th between the subarctic North Pacific and subtropical gyre, over lateral gradients in scavenging intensity similar to those found within the subarctic. This reflects a biogeochemical-province aspect to scavenging. Upper water column distributions of 231Pa and 231Pa/230Th ratio are consistent with the influence of scavenging by biogenic opal, while deep waters (>2.5 km) reveal an additional 231Pa sink possibly related to manganese oxides produced at continental margins or ridge crests.

Studies of the microbial diversity on analyzed samples from from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge

Marine sediments harbor an enormous quantity of microorganisms, including a multitude of novel species. The habitable zone of the marine sediment column begins at the sediment-water interface and probably extends to depths of several thousands of meters. Studies of the microbial diversity in this ecosystem have mostly relied on molecular biological techniques. We used a complementary method - analysis of intact polar membrane lipids - to characterize the in-situ microbial community in sediments covering a wide range of environmental conditions from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge. Bacterial and eukaryotic phospholipids were only detected in surface sediments from the Peru Margin. In contrast, deeply buried sediments, independent of their geographic location, were dominated by archaeal diether and tetraether lipids with various polar head groups and core lipids. We compared ring distributions of archaeal tetraether lipids derived from polar glycosidic precursors with those that are present as core lipids. The distributions of these related compound pools were distinct, suggestive of different archaeal sources, i.e., the polar compounds derive from sedimentary communities and the core lipids are fossil remnants from planktonic communities with possible admixtures of decayed sedimentary archaea. This in-situ production of distinct archaeal lipid populations potentially affects applications of the TEX86 paleotemperature proxy as demonstrated by offsets in reconstructed temperatures between both pools. We evaluated how varying cell and lipid stabilities will influence the sedimentary pool by using a box-model. The results are consistent with (i) a requirement of continuous inputs of freshly synthesized lipids in subsurface sediments for explaining the observed distribution of intact polar lipids, and (ii) decreasing lipid inputs with increasing burial depth.

Anelastic strain recovery and elastic properties of ODP Leg 123 oceanic basalt samples

A knowledge of rock stress is fundamental for improving our understanding of oceanic crustal mechanisms and lithospheric dynamic processes. However, direct measurements of stress in the deep oceans, and in particular stress magnitudes, have proved to be technically difficult. Anelastic strain recovery measurements were conducted on 15 basalt core samples from Sites 765 and 766 during Leg 123. Three sets of experiments were performed: anelastic strain recovery monitoring, dynamic elastic property measurements, and thermal azimuthal anisotropy observations. In addition, a range of other tests and observations were recorded to characterize each of the samples. One common feature of the experimental results and observations is that apparently no consistent orientation trend exists, either between the different measurements on each core sample or between the same sets of measurements on the various core samples. However, some evidence of correspondence between velocity anisotropy and anelastic strain recovery exists, but this is not consistent for all the core samples investigated. Thermal azimuthal anisotropy observations, although showing no conclusive correlations with the other results, were of significant interest in that they clearly exhibited anisotropic behavior. The apparent reproducibility of this behavior may point toward the possibility of rocks that retain a "memory" of their stress history, which could be exploited to derive stress orientations from archived core. Anelastic strain recovery is a relatively new technique. Because use of the method has extended to a wider range of rock types, the literature has begun to include examples of rocks that contracted with time. Strong circumstantial evidence exists to suggest that core-sample contractions result from the slow diffusion of pore fluids from a preexisting microcrack structure that permits the rock to deflate at a greater rate than the expansion caused by anelastic strain recovery. Both expansions and contractions of the Leg 123 cores were observed. The basalt cores have clearly been intersected by an abundance of preexisting fractures, some of which pass right through the samples, but many are intercepted or terminate within the rock matrix. Thus, the behavior of the core samples will be influenced not only by the properties of the rock matrix between the fractures, but also by how these macro- and micro-scale fractures mutually interact. The strain-recovery curves recorded during Leg 123 for each of the 15 basalt core samples may reflect the result of two competing time dependent processes: anelastic strain recovery and pore pressure recovery. Were these the only two processes to influence the gauge responses, then one might expect that given the additional information required, established theoretical models might be used to determine consistent stress orientations and reliable stress magnitudes. However, superimposed upon these competing processes is their respective interaction with the preexisting fractures that intersect each core. Evidence from our experiments and observations suggests that these fractures have a dominating influence on the characteristics of the recovery curves and that their effects are complex.

Stable oxygen isotope record of epibenthic foraminifera and water samples of the Arctic Ocean

We determined d18OCib values of live (Rose Bengal stained) and dead epibenthic foraminifera Cibicidoides wuellerstorfi, Cibicides lobatulus, and Cibicides refulgens in surface sediment samples from the Arctic Ocean and the Greenland, Iceland, and Norwegian seas (Nordic Sea). This is the first time that a comprehensive d18OCib data set is generated and compiled from the Arctic Ocean. For comparison, we defined Atlantic Water (AW), upper Arctic Bottom Water (uABW), and Arctic Bottom Water (ABW) by their temperature/salinity characteristics and calculated mean equilibrium calcite d18Oequ from summer sea-water d18Ow and in situ temperatures. As a result, in the Arctic environment we compensate for Cibicidoides- and Cibicides-specific offsets from equilibrium calcite of -0.35 and -0.55 per mil, respectively. After this taxon-specific adjustment, mean d18OCib values plausibly reflect the density stratification of principle water masses in the Nordic Sea and Arctic Ocean. In addition, mean d18OCib from AW not only significantly differs from mean d18OCib from ABW, but also d18OCib from within AW differentiates in function of provenience and water mass age. Furthermore, in shallow waters brine-derived low d18Ow can significantly lower the d18OCib of Cibicides spp. and thus d18OCib may serve as a paleobrine indicator. There is no statistically significant difference, however, between deeper water masses mean d18OCib of the Nordic Sea, and of the Eurasian and Amerasian basins, and no influence of low-d18Ow brines is recorded in Recent uABW and ABW d18OCib of C. wuellerstorfi. This may be due to dilution of a low-d18Ow brine signal in the deep sea, and/or to preferential incorporation of relatively high-d18Ow brines from high-salinity shelves. Although our data encompass environments with seasonal sea-ice and brine formation supposed to ultimately ventilate the deep Arctic Ocean, d18OCib from uABW and ABW do not indicate negative excursions. This may challenge hypotheses that call for enhanced Arctic brine release to explain negative benthic d18O spikes in deep-sea sediments from the late Pleistocene North Atlantic Ocean.

Geochemistry and radionuclide content of sediment and water samples obtained from the Ob and Irtysh river, Russia

This paper reports the results of the investigations of 2006-2007 on the distribution and migration forms of artificial radionuclides and chemical elements in the Ob-Irtysh water system. Three regions were studied. One of them is a local segment of the Ob River upstream from the confluence with the Irtysh River; its investigation allowed us to estimate the general radioecological state of the aquatic environment affected by the activity of the Tomsk 7 plant. The second region is a local segment of the Irtysh River upstream from its confluence with the Ob River, where the influence of emissions from the NPO Mayak could be estimated. The third region is the water area of the Ob River after its confluence with the Irtysh River. It characterizes the real level of radioactive and chemical contamination of the middle reaches of the Ob River. In order to explain horizontal variations in the distribution of radionuclides in the upper layer of bottom sediments collected at various sites, the results of sorption-kinetic experiments with radioactive tracers in the precipitate-solution system were used. The investigation of the migration forms of trace elements and radionuclides occurring in river water was based on the method of tangential-flow membrane filtration. Chemical element contents were determined in 400-ml water samples. A set of Millipore polysulfone membranes with pore sizes of 8, 1.2, 0.45, 0.1, and 0.025 µm was employed. Taking into account the ultralow specific concentrations of radionuclides in the water, they were analyzed in 300-500 litre samples using Millipore polysulfone membranes with pore sizes of 0.45 µm and 15 kDa. This allowed us to estimate the percentages of cesium-137 and plutonium-239, 240 in the suspended particulate fraction, colloids, and dissolved species.

Elements and isotopic measurements of magmatic rock samples from ODP Hole 104-642E

Trace element and isotopic signatures of magmatic rock samples from ODP Hole 642E at the Vøring Plateau provide insight into the interaction processes of mantle melt with crust during the initial magma extrusion phases at the onset of the continental breakup. The intermediate (basaltic-andesitic) to felsic (dacitic and rhyolitic) Lower Series magmas at ODP Hole 642E appear to be produced by large amounts of melting of upper crustal material. This study not only makes use of the traditional geochemical tools to investigate crust-mantle interaction, but also explores the value of Cs geochemistry as an additional tool. The element Cs forms the largest lithophile cation, and shows the largest contrast in concentration between (depleted) mantle and continental crust. As such it is a very sensitive indicator of involvement of crustal material. The Cs data reinforce the conclusion drawn from isotopic signatures that the felsic magmas are largely anatectic crustal melts. The down-hole geochemical variation within ODP Hole 642E defines a decreasing continental crustal influence from the Lower Series into the Upper Series. This is essential information to distinguish intrinsic geochemical properties of the mantle melts from signatures imposed by crustal contamination. A comparison with data from the SE Greenland margin highlights the compositional asymmetry of the crust-mantle interactions at both sides of the paleo-Iapetus suture. While Lower Series and Middle Series rocks from the SE Greenland margin have isotopic signatures reflecting interactions with lower and middle crust, such signatures have not been observed at the mid-Norwegian margin. The geochemical data either point to a dissimilar Caledonian crustal composition and/or to different geodynamic pre-breakup rifting history at the two NE Atlantic margin segments.

Chemistry of interstitial waters of samples from DSDP Leg 25

Interstitial water analyses from sediments collected during Leg 25 of the Deep Sea Drilling Project have revealed that in the southwest Indian Ocean, great chemical activity exists in sediments in various depositional environments. Variable sedimentation rates allow us to set some interesting boundary conditions on chemical and transport processes in these interstitial waters, particularly with regard to the distribution of dissolved sulfate. In terrigenous rapidly deposited sediments, large depletions are observed in magnesium and potassium, whereas relatively small decreases in dissolved calcium occur. In slowly deposited detrital sediments, also, large decreases in potassium and magnesium coincide with very large calcium increases. In truly pelagic sediments, a one to one replacement of magnesium by calcium is observed in the interstitial waters, presumably due to reactions in the basal sediment layers. Biogenous deposits have great influence on dissolved silica (sponge spicules and radiolarians) and on dissolved strontium (carbonate recrystallization). Otherwise, dissolved silica reflects the clay mineralogy and shows variations which seem particularly dependent on the presence or absence of kaolinite. Variable dissolved manganese values reflect reducing conditions and/or availability of manganese in the solid phases for mobilization in reducing sediments.

Late Neogene to Pleistocene palynology of ODP Leg 112 samples

The main objectives of this study are (1) to characterize the spatial and temporal variations in organic matter deposited in upwelling and related sediments (manifest in the palynoclast and organic-walled microplankton assemblages) and (2) to relate these variations to paleoenvironmental changes. A total of 40 samples from Holes 679D, 680B, 681B, 684B, 686B, and 687B were analyzed. Without exception, amorphogen dominates the palynoclast assemblages overwhelmingly. Influx of terrestrial particulate organic matter to the marine realm was extremely low. Levels of amorphogen swamp other palynoclast categories, and little significance can be attached to any variations observed. Microplankton dominate the palynomorph assemblages, with variable levels of subordinate foraminiferal test linings. Miospores are rare and are absent in most samples. Foraminiferal test linings are particularly abundant in the shallowest samples, which may reflect low surface-water paleotemperatures. Cysts of heterotrophic peridiniacean dinoflagellates (P-cysts) dominate the microplankton assemblages, with variable levels of cysts of autotrophic gonyaulacacean dinoflagellates (G-cysts). Samples dominated by P-cysts are derived largely from laminated, unbioturbated units deposited under the influence of strong upwelling. A lower abundance of P-cysts in some samples is restricted to unlaminated, bioturbated units deposited under oxygenated conditions. We conclude that the ratio of P-cysts to G-cysts is a useful indicator of variable upwelling strength. Detailed study of the variations in the microplankton assemblages offers one the greatest potential for palynological characteriztion and understanding of the upwelling system.

Lithium concentrations and isotope composition of basalt samples from ODP/DSDP Sites from Costa Rica Rift

Ocean Drilling Program (ODP) Hole 504B near the Costa Rica Rift is the deepest hole drilled in the ocean crust, penetrating a volcanic section, a transition zone and a sheeted dike complex. The distribution of Li and its isotopes through this 1.8-km section of oceanic crust reflects the varying conditions of seawater alteration with depth. The upper volcanic rocks, altered at low temperatures, are enriched in Li (5.6-27.3 ppm) and have heavier isotopic compositions (delta7Li=6.6-20.8?) relative to fresh mid-ocean ridge basalt (MORB) due to uptake of seawater Li into alteration clays. The Li content and isotopic compositions of the deeper volcanic rocks are similar to MORB, reflecting restricted seawater circulation in this section. The transition zone is a region of mixing of seawater with upwelling hydrothermal fluids and sulfide mineralization. Li enrichment in this zone is accompanied by relatively light isotopic compositions (-0.8-2.1?) which signify influence of basalt-derived Li during mineralization and alteration. Li decreases with depth to 0.6 ppm in the sheeted dike complex as a result of increasing hydrothermal extraction in the high-temperature reaction zone. Rocks in the dike complex have variable isotopic values that range from -1.7 to 7.9?, depending on the extent of hydrothermal recrystallization and off-axis low-temperature alteration. Hydrothermally altered rocks are isotopically light because 6Li is preferentially retained in greenschist and amphibolite facies minerals. The delta7Li values of the highly altered rocks of the dike complex are complementary to those of high-temperature mid-ocean ridge vent fluids and compatible to equilibrium control by the alteration mineral assemblage. The inventory of Li in basement rocks permits a reevaluation of the role of oceanic crust in the budget of Li in the ocean. On balance, the upper 1.8 km of oceanic crusts remains a sink for oceanic Li. The observations at 504B and an estimated flux from the underlying 0.5 km of gabbro suggest that the global hydrothermal flux is at most 8*10**9 mol/yr, compatible with geophysical thermal models. This work defines the distribution of Li and its isotopes in the upper ocean crust and provides a basis to interpret the contribution of subducted lithosphere to arc magmas and cycling of crustal material in the deep mantle.

(Table 1) 87Sr/86Sr ratios and ages of DSDP Site 144A samples

Glassy Turonian foraminifera preserved in clay-rich sediments from the western tropical Atlantic yield the warmest equivalent d18O sea-surface temperatures (SSTs) yet reported for the entire Cretaceous-Cenozoic. We estimate Turonian SSTs that were at least as warm as (conservative mean ~30 °C) to significantly warmer (warm mean ~33 °C) than those in the region today. However, if independent evidence for high middle Cretaceous pCO2 is reliable and resulted in greater isotopic fractionation between seawater and calcite because of lower sea-surface pH, our conservative and warm SST estimates would be even higher (32 and 36°C, respectively). Our new tropical SSTs help reconcile geologic data with the predictions of general circulation models that incorporate high Cretaceous pCO2 and lend support to the hypothesis of a Cretaceous greenhouse. Our data also strengthen the case for a Turonian age for the Cretaceous thermal maximum and highlight a 20-40 m.y. mismatch between peak Cretaceous-Cenozoic global warmth and peak inferred tectonic CO2 production. We infer that this mismatch is either an artifact of a hidden Turonian pulse in global ocean-crust cycling or real evidence of the influence of some other factor on atmospheric CO2 and/or SSTs. A hidden pulse in crust cycling would explain the timing of peak Cretaceous-Cenozoic sea level (also Turonian), but other factors are needed to explain high-frequency (~10-100 k.y.) instability in middle Cretaceous SSTs reported elsewhere.

Physical properties and hexachlorocyclohexane concentrations of sea-ice, water and ice algae samples, eastern Beaufort Sea

We present evidence that both geophysical and thermodynamic conditions in sea ice are important in understanding pathways of accumulation or rejection of hexachlorocyclohexanes (HCHs). a- and g-HCH concentrations and a-HCH enantiomer fractions have been measured in various ice classes and ages from the Canadian High Arctic. Mean a-HCH concentrations reached 0.642 ± 0.046 ng/L in new and young ice (<30 cm), 0.261 ±0.015 ng/L in the first-year ice (30-200 cm) and 0.208 ±0.045 in the old ice (>200 cm). Mean g-HCH concentrations were 0.066 ± 0.006 ng/L in new and young ice, 0.040 ±0.002 ng/L in the first-year ice and 0.040 ±0.007 ng/L in the old ice. In general, a-HCH concentrations and vertical distributions were highly dependent on the initial entrapment of brine and the subsequent desalination process. g-HCH levels and distribution in sea ice were not as clearly related to ice formation processes. During the year, first-year ice progressed from freezing (accumulation) to melting (ablation). Relations between the geophysical state of the sea ice and the vertical distribution of HCHs are described as ice passes through these thermodynamic states. In melting ice, which corresponded to the algal bloom period, the influence of biological processes within the bottom part of the ice on HCH concentrations and a-HCH enantiomer fraction is discussed using both univariate and multivariate approaches.