bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress State in the Kumano Basin and in Slope Sediment Determined From Anelastic Strain Recovery: Results From IODP Expedition 338 to the Nankai Trough
Authors: Oohashi Kiyokazu , Lin Weiren , Wu Hung‐Yu , Yamaguchi Asuka , Yamamoto Yuhji 
Published: September 2017

AbstractThree‐dimensional, in situ stresses in the Kumano Basin and slope sediment (IODP Sites C0002 and C0022) in the Nankai Trough, southwest Japan, have been determined using the anelastic strain recovery (ASR) of core samples. Two samples taken from Hole C0002J, located in the bottom of the Kumano Basin, indicate that the maximum principal stress, σ1, is vertical. The intermediate principal stress, σ2, is oriented ENE–WSW, parallel to the trench axis. These stress orientations are similar to those obtained using ASR and borehole breakout methods in previous expeditions. In contrast, a sample from the lower section of the slope sediment (Hole C0022B), located beneath the megasplay fault, is characterized by σ1 plunging moderately to the ESE and σ3 oriented near‐horizontally, trending NNE–SSW. The direction of maximum horizontal stress obtained from ASR (WNW–ESE) is similar to that inferred from borehole breakouts in an adjacent hole (NW–SE). Trench‐normal compression and a near‐vertical σ2 are also inferred from focal mechanisms of very‐low‐frequency earthquakes within the Nankai accretionary prism, and from borehole breakouts in the hanging wall of the megasplay fault. These observations suggest that the horizontal compressional regime extends to a shallower level than previously thought, likely due to the shallow portion of the megasplay fault accumulating tectonic stress in response to plate convergence.
The Warm Plasma Composition in the Inner Magnetosphere During 2012–2015
Authors: Jahn J.‐M. , Goldstein J. , Reeves G. D. , Fernandes P. A. , Skoug R. M. , Larsen B. A , Spence H. E. 
Published: September 2017

AbstractIonospheric heavy ions play an important role in the dynamics of Earth's magnetosphere. The greater mass and gyroradius of ionospheric oxygen differentiates its behavior from protons at the same energies. Oxygen may have an impact on tail reconnection processes, and it can at least temporarily dominate the energy content of the ring current during geomagnetic storms. At sub‐keV energies, multispecies ion populations in the inner magnetosphere form the warm plasma cloak, occupying the energy range between the plasmasphere and the ring current. Lastly, cold lighter ions from the midlatitude ionosphere create the corotating plasmasphere whose outer regions can interact with the plasma cloak, plasma sheet, ring current, and outer electron belt. In this paper we present a statistical view of warm, cloak‐like ion populations in the inner magnetosphere, contrasting, in particular, the warm plasma composition during quiet and active times. We study the relative abundances and absolute densities of warm plasma measured by the Van Allen Probes, whose two spacecraft cover the inner magnetosphere from plasmaspheric altitudes close to Earth to just inside geostationary orbit. We observe that warm (>30 eV) oxygen is most abundant closer to the plasmasphere boundary, whereas warm hydrogen dominates closer to geostationary orbit. Warm helium is usually a minor constituent but shows a noticeable enhancement in the near‐Earth dusk sector.
A Three‐Dimensional Model of Pluto's Interaction With the Solar Wind During the New Horizons Encounter
Authors: Feyerabend Moritz , Liuzzo Lucas , Simon Sven , Motschmann Uwe 
Published: September 2017

AbstractWe apply a hybrid (kinetic ions and fluid electrons) simulation model to study Pluto's plasma environment during the New Horizons encounter on 14 July 2015. We show that Pluto's plasma interaction is dominated by significant north‐south asymmetries, driven by large pickup ion gyroradii on the order of 200 Pluto radii. The transition region from the ambient solar wind to the population of plutogenic ions (called the “Plutopause”) also shows considerable asymmetries that cannot be explained by a fluid picture. Since the New Horizons spacecraft does not carry a magnetometer, we use our model to estimate the strength and direction of the interplanetary magnetic field (IMF) at the time of the flyby by comparing output from the hybrid simulation to the plasma signatures observed during the New Horizons encounter. We find that an IMF strength of at least 0.24 nT is required to generate the observed plasma signatures. An IMF orientation either parallel or antiparallel to Pluto's orbital motion is able to explain the observed plasma densities and velocities along the New Horizons trajectory. Our simulations are able to quantitatively reproduce all key features of the plasma observations, specifically the gradual slowing of the solar wind, as well as the location and thickness of the Plutopause and bow shock.
Observation of Three‐Dimensional Magnetic Reconnection in the Terrestrial Magnetotail
Authors: Zhou Meng , Ashour‐Abdalla Maha , Deng Xiaohua , Pang Ye , Fu Huishan , Walker Raymond , Lapenta Giovanni , Huang Shiyong , Xu Xiaojun , Tang Rongxin 
Published: September 2017

AbstractStudy of magnetic reconnection has been focused on two‐dimensional geometry in the past decades, whereas three‐dimensional structures and dynamics of reconnection X line are poorly understood. In this paper, we report Cluster multispacecraft observations of a three‐dimensional magnetic reconnection X line with a weak guide field (~25% of the upstream magnetic field) in the Earth's magnetotail. We find that the X line not only retreated tailward but also expanded across the tail following the electron flow direction with a maximum average speed of (0.04–0.15) VA,up, where VA,up is the upstream Alfvén speed, or (0.14–0.57) Vde, where Vde is the electron flow speed in the out‐of‐plane direction. An ion diffusion region was observed by two spacecraft that were separated about 10 ion inertial lengths along the out‐of‐plane direction; however, these two spacecraft observed distinct magnetic structures associated with reconnection: one spacecraft observed dipolarization fronts, while the other one observed flux ropes. This indicates that reconnection proceeds in drastically different ways in different segments along the X line only a few ion inertial lengths apart.
Dominant Controls of Downdip Afterslip and Viscous Relaxation on the Postseismic Displacements Following the Mw7.9 Gorkha, Nepal, Earthquake
Authors: Zhao Bin , Bürgmann Roland , Wang Dongzhen , Tan Kai , Du Ruilin , Zhang Rui 
Published: September 2017

AbstractWe analyze three‐dimensional GPS coordinate time series from continuously operating stations in Nepal and South Tibet and calculate the initial 1 year postseismic displacements. We first investigate models of poroelastic rebound, afterslip, and viscoelastic relaxation individually and then attempt to resolve the trade‐offs between their contributions by evaluating the misfit between observed and simulated displacements. We compare kinematic inversions for distributed afterslip with stress‐driven afterslip models. The modeling results show that no single mechanism satisfactorily explains near‐ and far‐field postseismic deformation following the Gorkha earthquake. When considering contributions from all three mechanisms, we favor a combination of viscoelastic relaxation and afterslip alone, as poroelastic rebound always worsens the misfit. The combined model does not improve the data misfit significantly, but the inverted afterslip distribution is more physically plausible. The inverted afterslip favors slip within the brittle‐ductile transition zone downdip of the coseismic rupture and fills the small gap between the mainshock and largest aftershock slip zone, releasing only 7% of the coseismic moment. Our preferred model also illuminates the laterally heterogeneous rheological structure between India and the South Tibet. The transient and steady state viscosities of the upper mantle beneath Tibet are constrained to be greater than 1018 Pa s and 1019 Pa s, whereas the Indian upper mantle has a high viscosity ≥1020 Pa s. The viscosity in the lower crust of southern Tibet shows a clear trade‐off with its southward extent and thickness, suggesting an upper bound value of ~8 × 1019 Pa s for its steady state viscosity.
Tectonic Stacking of HP/LT Metamorphic Rocks in Accretionary Wedges and the Role of Shallowing Slab‐Mantle Decoupling
Authors: Aygül Mesut , Oberhänsli Roland 
Published: September 2017

AbstractHigh‐pressure/low‐temperature (HP/LT) chloritoid‐bearing micaschists crop out widely in the central part of northern Turkey and represent deep‐seated subduction‐accretionary complexes. Three peak metamorphic assemblages are identified in the area studied: (1) garnet‐chloritoid‐glaucophane with pseudomorphs after lawsonite; (2) chloritoid with pseudomorphs after glaucophane; and (3) chloritoid with pseudomorphs after jadeite in addition to phengite, paragonite, quartz, chlorite, rutile, and apatite. The latter is interpreted as transformation of a chloritoid + glaucophane assemblage to chloritoid + jadeite with increasing pressure; PT modeling indicates ~17 and 22–25 kbars for the two peak parageneses. The diversity of peak metamorphic assemblages and the PT estimates suggest that basal accretion occurred at different depths within the wedge. The depth of the basal accretion is possibly controlled by the slab‐mantle decoupling depth. Stretching and thinning of the lithospheric fore arc induced by the slab rollback possibly caused shallowing of the slab‐mantle decoupling depth which limited depth of the basal accretion from 70–80 km to ~55 km within the subduction channel. A slab‐mantle coupling depth‐controlled basal accretion may also explain the scarcity of eclogite and high‐grade blueschist facies metamorphic rocks in active intraoceanic subduction zones. Because the overriding plate is young and hot in intraoceanic subductions, the slab and mantle are coupled at a relatively shallow depth before eclogitization of the oceanic crust. This prevents accretion and exhumation of eclogite along the subduction channel.
The Rangeland Hydrology and Erosion Model: A Dynamic Approach for Predicting Soil Loss on Rangelands
Authors: Hernandez Mariano , Nearing Mark A. , Al‐Hamdan Osama Z. , Pierson Frederick B. , Armendariz Gerardo , Weltz Mark A. , Spaeth Kenneth E. , Williams C. Jason , Nouwakpo Sayjro K. , Goodrich David C. , Unkrich Carl L. , Nichols Mary H. , Holifield Collins Chandra D. 
Published: September 2017

AbstractIn this study, we present the improved Rangeland Hydrology and Erosion Model (RHEM V2.3), a process‐based erosion prediction tool specific for rangeland application. The article provides the mathematical formulation of the model and parameter estimation equations. Model performance is assessed against data collected from 23 runoff and sediment events in a shrub‐dominated semiarid watershed in Arizona, USA. To evaluate the model, two sets of primary model parameters were determined using the RHEM V2.3 and RHEM V1.0 parameter estimation equations. Testing of the parameters indicated that RHEM V2.3 parameter estimation equations provided a 76% improvement over RHEM V1.0 parameter estimation equations. Second, the RHEM V2.3 model was calibrated to measurements from the watershed. The parameters estimated by the new equations were within the lowest and highest values of the calibrated parameter set. These results suggest that the new parameter estimation equations can be applied for this environment to predict sediment yield at the hillslope scale. Furthermore, we also applied the RHEM V2.3 to demonstrate the response of the model as a function of foliar cover and ground cover for 124 data points across Arizona and New Mexico. The dependence of average sediment yield on surface ground cover was moderately stronger than that on foliar cover. These results demonstrate that RHEM V2.3 predicts runoff volume, peak runoff, and sediment yield with sufficient accuracy for broad application to assess and manage rangeland systems.
FeSCluster Assembly:ISCSystem in Bacteria and Eukarya
Authors: de Choudens Sandrine Ollagnier , Puccio Hélène 
Published: September 2017

AbstractIron–sulfur clusters are key cofactors in proteins involved in a large number of conserved cellular processes, including gene expression, DNA replication and repair, ribosome biogenesis, tRNA modification, central metabolism, and respiration. Fe–S proteins can perform a wide range of functions, from electron transfer to redox and nonredox catalysis. In all living organisms, Fe–S proteins are first synthesized in an apoform. However, as the Fe–S prosthetic group is required for correct folding and/or protein stability, Fe–S clusters are inserted co‐translationally or immediately after translation by specific assembly machineries. These systems have been extensively studied over the last decade, both in prokaryotes and eukaryotes. This chapter covers the basic principles of the Fe/S biogenesis ISC (iron–sulfur cluster) machinery and the most exciting recent highlights relating to this system. These advances enhance our understanding of the Fe–S cluster assembly mechanism.
FeSCluster Assembly: Role of MonothiolGrxsandNfuProteins
Authors: Przybyla‐Toscano Jonathan , Roret Thomas , Couturier Jérémy , Rouhier Nicolas 
Published: September 2017

AbstractThe cellular maturation of iron–sulfur (Fe–S) proteins necessitates dedicated assembly machineries. In eukaryotes, the ISC (iron–sulfur cluster) and SUF (sulfur mobilization) machineries are autonomous biogenesis systems for mitochondrial and chloroplastic proteins respectively, whereas the cytosolic CIA (cytosolic iron–sulfur cluster assembly) machinery operates for cytosolic and nuclear proteins and depends on the ISC machinery for obtaining the required labile sulfur atoms. Owing to their capacity to incorporate Fe–S clusters alone or in complex with BOLA proteins, class II glutaredoxins (GRXs) play some key roles in this maturation process, although the precise roles have yet to be clearly delineated. Organellar GRXs likely serve as Fe–S transfer proteins, accepting preformed Fe–S clusters from scaffold proteins used for theirde novosynthesis before delivering them to other ISC or SUF targeting factors such as ISCA proteins or to final client proteins. The cytosolic/nuclear localized GRXs seem to have at least three different crucial roles, likely originating from their key position connecting the ISC machinery to the cytosolic compartment. Indeed, the molecular analysis of yeast mutants suggests that it could be the primary recipient protein of the unknown sulfur compound exported from the mitochondria and which could serve to assemble its Fe–S cluster. The presence of the cluster seems mandatory for all identified functions, serving (i) for the maturation of Fe–S clusters in the CIA electron donor DRE2, (ii) for the regulation of iron homeostasis in conjunction with BOLA and the Aft1/2 transcriptional regulators, and (iii) for the proper distribution of iron and correct functioning of all iron‐dependent proteins. These roles might not all be evolutionary conserved, notably in plants. In addition to providing an overview of the known physiological roles of class II GRXs, we describe their biochemical and structural properties focusing in particular on their interaction with other maturation factors of the BOLA, DRE2, and ISCA families.
Assembly of Hemea3‐CuBandCuAin CytochromecOxidase
Authors: Nyvltova Eva , Barrientos Antoni , Hosler Jonathan 
Published: September 2017

AbstractTheaa3‐type cytochromecoxidase (CcO) is a heme–copper terminal oxidase present in many bacteria, particularly theα‐proteobacteria, and in all mitochondria, which arose from theα‐proteobacteria. CcO is a multimeric enzyme, but all of its redox‐active metal centers are located within subunits 1 and 2, termed COX1 and COX2. The structure of the redox‐active metal centers is completely conserved fromα‐proteobacteria to humans. Assembly of the metal centers of CcO requires a group of proteins dedicated to the process, the numbers of which always exceed the number of CcO structural subunits. Five key assembly proteins from theα‐proteobacteria are also present in mitochondria, but the assembly machinery in mitochondria is much more elaborate and thus requires many more assembly factors. In addition, copper homeostasis in mitochondria is highly regulated and coupled to metal incorporation into CcO. Although investigations over the last 50 years have disclosed the sophistication of the pathways involved in the assembly of the redox‐active metal centers of CcO, numerous questions remain. Here, we review the current state of knowledge of the biogenesis and assembly of the catalytic core of CcO and examine the mechanisms of metal center assembly operating in prokaryotes and eukaryotes.
Assembly ofCuZandCuAin Nitrous Oxide Reductase
Authors: Pauleta Sofia R. , Moura Isabel 
Published: September 2017

AbstractNitrous oxide (N2O) reductase is a copper enzyme that catalyzes the reduction of N2O to dinitrogen, the last step of the denitrification pathway. This enzyme has two copper centers: a CuA center that is the electron transfer center and the “CuZ center” where the catalysis occurs. This enzyme has been the center of several studies over the last 20 years, and many of its spectroscopic and catalytic properties have been determined, as well as its structure in different oxidation states. These studies have also revealed that the CuA center is similar to the one present in cytochromecoxidase, being a binuclear copper center, while the CuZ center is unique in biology, being a tetranuclear copper center bridged by a sulfur atom. Moreover, these studies have also identified that the CuZ center can exist in two forms, CuZ*(4Cu1S) and CuZ(4Cu2S). The first has a high turnover number in the fully reduced state, while the CuZ(4Cu2S) form of CuZ center has a very small turnover number and cannot explain the high capacity of the whole cells in reducing N2O, from which the enzyme is isolated with CuZ center mainly in that form. This fact envisages an activation mechanism still to be unraveled that might involve one or more enzymes/proteins encoded by thenosgenes and a putative sulfur‐displacement mechanism.The biogenesis of these two centers has not been extensively studied, and at least with respect to the copper insertion, it has been postulated that there are alternative routes. The apo‐N2OR is synthesized in the cytoplasm in the apo form and is transported to the periplasmic space by either the Sec (unfolded state) or Tat system (dimer folded state), where the centers are assembled. Thus, CuA assembly has been proposed to be dependent on a copper chaperone, pCuAC, and Sco, a thiol‐disulfide reductase that reduces the disulfide bridge between the two cysteines in the apo‐CuA center. Relative to the CuZ center, the delivery of copper atoms is by NosL, an outer‐membrane protein, while the sulfur atoms are transported by the ABC transporter encoded bynosDFYgenes. The other accessory proteins NosR and NosX have been assigned broader functions. NosR has been implicated innosZexpression, as well as in maintaining the activity of N2OR, a function that has been shared by NosX.In this chapter the main biochemical properties of N2OR, as well as the biogenesis of its two copper centers, will be reviewed.
Heme Biosynthesis and Insertion
Authors: Medlock Amy E. , Dailey Harry A. 
Published: September 2017

Abstract

Protoheme IX (heme) is a versatile cofactor that is required and synthesized by most organisms. It is a member of the tetrapyrrole family of cofactors that also includes siroheme, factor F
430
, heme d
1
, chlorophyll, and cobalamin. Heme is a porphyrin with a central iron atom bound by the nitrogen atoms of the pyrrole rings. The versatility of heme is apparent in the diverse reactions that it can participate in as a protein cofactor. Recently studies on the biosynthesis of heme have been rejuvenated with the discovery and description of two pathways by which some organisms synthesize heme. The oldest and best studied heme biosynthetic pathway is the protoporphyrin‐dependent (PPD) pathway, previously called the classic pathway. This is used by eukaryotes and most Gram‐negative bacteria. A second pathway has siroheme as an intermediate to produce heme. This pathway, called the siroheme‐dependent (SHD) or alternate heme biosynthesis pathway, is present in sulfite‐reducing bacteria and some Archaea. The most recently described pathway is the coproporphyrin‐dependent (CPD) pathway. It is present in Gram‐positive bacteria and some transitional Gram‐negative bacteria. Each of these pathways begins with the synthesis of aminolevulinic acid, the first committed intermediate in heme synthesis, and proceeds to the cyclic tetrapyrrole uroporphyrinogen III. At this point, the SHD pathway branches, while the PPD and CPD pathways proceed through an additional common step to produce coproporphyinogen III. The PPD and CPD pathways then branch to produce heme in three additional steps each. In contrast to our knowledge of the individual enzymes of the biosynthetic pathways, less is known about pathway regulation for most organisms. This chapter presents an overview of what is currently known about heme biosynthesis and its regulation in diverse organisms.
F430 Biosynthesis and Insertion
Authors: Mansoorabadi Steven O. , Zheng Kaiyuan , Ngo Phong D. 
Published: September 2017

AbstractMethyl‐coenzyme M reductase (MCR) is the key enzyme of methanogenesis and the anaerobic oxidation of methane (AOM). MCR catalyzes the reversible conversion of methyl‐coenzyme M (MeS‐CoM) and coenzyme B (CoB‐SH) to the mixed heterodisulfide, CoB‐S‐S‐CoM, and methane. The methane forming and oxidizing activities of MCR are dependent on the unique, nickel‐containing tetrapyrrole, coenzyme F430. In addition to housing F430, the active site regions of MCR from both methanogens and anaerobic methanotrophic archaea (ANME) contain several unusual posttranslational modifications (PTMs). Given the unique ability of MCR to catalyze the AOM, there is much interest in the mechanism and formation ofholoMCR for potential applications in gas‐to‐liquid (GTL) conversion strategies (seeMethane‐to‐Methanol Conversion). This chapter details current progress in the understanding of coenzyme F430 biosynthesis, the maturation of MCR, and differences in structural features of methanogenic and methanotrophic MCR that may be important for the AOM.
Formation of Crosslinked
Cys–Tyr
Free Radical Redox Cofactor
Authors: Whittaker James W. 
Published: September 2017

Abstract

The cysteinyl–tyrosine (Cys–Tyr) amino acid dimer is one of the simplest redox cofactors in biology, essential for the activity of a phylogenetically diverse family of copper metalloradical oxidase enzymes, including galactose oxidase. Formation of the Cys–Tyr cofactor is programmed into the structure of the protein, which undergoes spontaneous self‐processing to crosslink two amino acids (Cys, Tyr) in the polypeptide chain. The covalent crosslink alters the properties of the tyrosine side chain and creates an intrinsic redox cofactor in the protein capable of undergoing a 1‐electron redox cycle, stabilizing a modified phenoxyl free radical for catalysis. Although it is unusual, the crosslinking reaction reflects fundamental aspects of protein chemistry, and it is likely that this type of cofactor has arisen multiple times in evolution. A related Cys–Tyr crosslink feature has been found in the outer sphere of non‐heme iron oxygenases, but in that context it appears to have a different function and is not essential for catalysis. The mechanism of Cys–Tyr biogenesis has been most extensively investigated for galactose oxidase, where biochemical, structural, spectroscopic and kinetic approaches have been used to provide insight into the elementary steps responsible for creation of the redox cofactor. The experimentally defined pathway for efficient cofactor biogenesis involves protein folding, coordination of reduced (Cu
I
) metal ion, and dioxygen activation.