Lawrence Head Volcanics and Dunnage Mélange, Newfoundland Appalachians: Origin by Ordovician Ridge Subduction or in Back-Arc Rift?

This paper reviews the geological setting and reports new geochemical trace element data from the Ordovician Lawrence Head Volcanics (LHV) and the underlying gabbro sills in the Exploits Group. In combination with existing published analyses and ages of these rocks, the volcanic rocks and sills are indistinguishable in composition and age, and the data are consistent with the hypothesis that they represent the same (mostly E-MORB composition) magmatic event in the early–mid Darriwilian (~465 ± 2 Ma). The LHV and their enclosing strata show regional evidence for: 1) upward decline of volume and grain size of arc-derived volcaniclastic materials over the uppermost interval of turbidite sedimentary strata below the LHV; 2) change to shallow marine conditions locally by the end of the LHV event, followed immediately by significant subsidence, and 3) no evidence of coarse-grained clastic input, nor of normal faulting, during or immediately after LHV magmatism. Ridge–trench interaction (ridge subduction) at a subduction system is consistent with all of these features and spatial distribution of related elements, but a rift (back-arc) origin over a subduction zone can only accommodate the compositions, and is inconsistent with the geological evidence. The Dunnage Mélange (DM) has been interpreted either as olistostromal in a developing back-arc rift basin, or as a subduction accretionary prism. Peraluminous intrusions in the mélange (Coaker Porphyry ― CP) are more readily explained by ridge subduction, and a previously reported zircon age (469 ± 4 Ma) is consistent with the age of the LHV and gabbro sills, also interpreted as products of ridge subduction. Localization of the CP in the eastern area of DM, and of most of the large LHV-derived volcanic blocks in the western DM, suggests a slightly younger age, and perhaps a different mechanism, for the origin of the western DM.SOMMAIRECet article passe en revue le contexte géologique et présente de nouvelles données géochimiques d’éléments traces des roches volcaniques ordoviciennes de Lawrence Head (LHV) et des filons-couches de gabbro sous-jacents du Groupe Exploits.  Considérant la combinaison des données d’analyse publiées et des datations de ces roches, les roches volcaniques et les filons-couches sont indiscernables tant en composition qu’en âge, et les données sont compatibles avec l’hypothèse selon laquelle ils représentent le même événement magmatique (principalement E-MORB) du Darriwilien précoce à moyen (~465 ± 2 Ma).  Les LHV ainsi que les strates de l’encaissant renferment des indices régionaux qui montrent : 1) que le volume et la granulométrie des matériaux volcanoclastiques d’arc diminuent vers le haut dans l’intervalle supérieur des strates de turbidites sédimentaires sous les LHV; 2) que le changement vers des milieux marins peu profonds localement vers la fin de l’événement des LHV a été suivi immédiatement par une subsidence importante, et 3) qu’il n’existe pas d’indices d’apports clastiques à gros grains, non plus que de formation de failles normales, durant ou immédiatement après le magmatisme des LHV.  L’interaction crête-fosse (subduction de la crête) au lieu d’un système de subduction concorde avec toutes ces caractéristiques et la répartition spatiale des éléments reliés, alors qu’une origine de crête (arrière-arc) au-dessus d’une zone de subduction ne peut expliquer que les compositions et qu’elle est incompatible avec l’évidence géologique.  Le Dunnage Mélange (DM) a été interprété soit comme un olistostome dans un bassin d’arrière-arc en développement, ou comme un prisme d’accrétion de subduction.  Les intrusions hyperalumineuses dans le mélange (Porphyre Coaker — CP), s’explique plus facilement par une subduction de crête, et un âge de datation sur zircon de (469 ± 4 Ma) correspond à l’âge des LHV et des filons-couche de gabbro, aussi interprétés comme produits d’une subduction de crête.  La localisation du CP dans la portion orientale du DM, et de la majeure partie des grands blocs volcaniques dérivés des LHV de la portion ouest du DM, suggère un âge légèrement plus jeune, et peut-être un mécanisme différent, pour l’origine de la portion ouest du DM

A statistical framework to evaluate virtual screening

<p>Abstract</p> <p>Background</p> <p>Receiver operating characteristic (ROC) curve is widely used to evaluate virtual screening (VS) studies. However, the method fails to address the "early recognition" problem specific to VS. Although many other metrics, such as RIE, BEDROC, and pROC that emphasize "early recognition" have been proposed, there are no rigorous statistical guidelines for determining the thresholds and performing significance tests. Also no comparisons have been made between these metrics under a statistical framework to better understand their performances.</p> <p>Results</p> <p>We have proposed a statistical framework to evaluate VS studies by which the threshold to determine whether a ranking method is better than random ranking can be derived by bootstrap simulations and 2 ranking methods can be compared by permutation test. We found that different metrics emphasize "early recognition" differently. BEDROC and RIE are 2 statistically equivalent metrics. Our newly proposed metric SLR is superior to pROC. Through extensive simulations, we observed a "seesaw effect" – overemphasizing early recognition reduces the statistical power of a metric to detect true early recognitions.</p> <p>Conclusion</p> <p>The statistical framework developed and tested by us is applicable to any other metric as well, even if their exact distribution is unknown. Under this framework, a threshold can be easily selected according to a pre-specified type I error rate and statistical comparisons between 2 ranking methods becomes possible. The theoretical null distribution of SLR metric is available so that the threshold of SLR can be exactly determined without resorting to bootstrap simulations, which makes it easy to use in practical virtual screening studies.</p

Controlled Experiments of Hillslope Coevolution at the Biosphere 2 Landscape Evolution Observatory: Toward Prediction of Coupled Hydrological, Biogeochemical, and Ecological Change

Understanding the process interactions and feedbacks among water, porous geological media, microbes, and vascular plants is crucial for improving predictions of the response of Earth’s critical zone to future climatic conditions. However, the integrated coevolution of landscapes under change is notoriously difficult to investigate. Laboratory studies are limited in spatial and temporal scale, while field studies lack observational density and control. To bridge the gap between controlled laboratory and uncontrollable field studies, the University of Arizona built a macrocosm experiment of unprecedented scale: the Landscape Evolution Observatory (LEO). LEO comprises three replicated, heavily instrumented, hillslope-scale model landscapes within the environmentally controlled Biosphere 2 facility. The model landscapes were designed to initially be simple and purely abiotic, enabling scientists to observe each step in the landscapes’ evolution as they undergo physical, chemical, and biological changes over many years. This chapter describes the model systems and associated research facilities and illustrates how LEO allows for tracking of multiscale matter and energy fluxes at a level of detail impossible in field experiments. Initial sensor, sampler, and soil coring data are already providing insights into the tight linkages between water flow, weathering, and microbial community development. These interacting processes are anticipated to drive the model systems to increasingly complex states and will be impacted by the introduction of vascular plants and changes in climatic regimes over the years to come. By intensively monitoring the evolutionary trajectory, integrating data with mathematical models, and fostering community-wide collaborations, we envision that emergent landscape structures and functions can be linked, and significant progress can be made toward predicting the coupled hydro-biogeochemical and ecological responses to global change

A genomic storm in critically injured humans

Critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean : phylogeny, physiology and stable isotope fractionation

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1796–1808, doi:10.1038/ismej.2011.58.Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the north Pacific Ocean that have been maintained in laboratory culture for over three years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S rRNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and cDNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonium (NH4 +) to nitrite (NO2 -). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13- 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.This work was supported by a Woods Hole Oceanographic Institution (WHOI) Postdoctoral Scholar fellowship to AES and the WHOI Ocean Life Institute

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments

First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

We would like to thank Frederick (Rick) Colwell for input on molecular analyses in low biomass environments, Donna Blackman, Benoît Ildefonse, Adélie Delacour, and Gretchen Früh-Green for discussions regarding geological and geochemical aspects of this manuscript, and the Integrated Ocean Drilling Program Expeditions 304/305 Science Party. We would also like to thank Captain Alex Simpson and the entire crew of the JOIDES Resolution.Conceived and designed the experiments: OUM MRF SJG. Performed the experiments: OUM TN MR JDVN AM. Analyzed the data: OUM TN MR JDVN AM. Contributed reagents/materials/analysis tools: TN MR JZ MRF SJG. Wrote the paper: OUM.The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.Yeshttp://www.plosone.org/static/editorial#pee

Shroud of lecturing

The Web challenges the authority of the professor in the classroom by democratizing information. It shifts the focus from professor and lecture to student and information. The culture of higher education is likely to be profoundly changed as a result