High-resolution IP25 of three sediment cores in the western North Pacific and Bering Sea

Due to its strong influence on heat and moisture exchange between the ocean and the atmosphere, sea ice is an essential component of the global climate system. In the context of its alarming decrease in terms of concentration, thickness and duration, understanding the processes controlling sea-ice variability and reconstructing paleo-sea-ice extent in polar regions have become of great interest for the scientific community. In this study, for the first time, IP25, a recently developed biomarker sea-ice proxy, was used for a high-resolution reconstruction of the sea-ice extent and its variability in the western North Pacific and western Bering Sea during the past 18,000 years. To identify mechanisms controlling the sea-ice variability, IP25 data were associated with published sea-surface temperature as well as diatom and biogenic opal data. The results indicate that a seasonal sea-ice cover existed during cold periods (Heinrich Stadial 1 and Younger Dryas), whereas during warmer intervals (Bølling-Allerød and Holocene) reduced sea ice or ice-free conditions prevailed in the study area. The variability in sea-ice extent seems to be linked to climate anomalies and sea-level changes controlling the oceanographic circulation between the subarctic Pacific and the Bering Sea, especially the Alaskan Stream injection though the Aleutian passes.

High-resolution sediment record from a submarine meandering canyon system in the eastern Atlantic

Based on a high-resolution sediment record from a submarine meandering canyon system offshore the present-day hyperarid Saharan Africa, two phases of turbidity-current activity can be distinguished during the past 13,000 years. Frequent, siliciclastic turbidity currents can be related to deglacial sea-level history, whereas rhythmically recurring fine-grained and carbonate-rich turbidity currents with recurrence times of roughly 900 years are inferred for the Holocene. Various trigger mechanisms can be considered to initiate turbidity currents, but only a few can explain a periodic turbidite activity. A comparison of Holocene turbidite recurrence times and basic cycles of 900 and 1,800 years found in various Holocene paleoclimate studies suggests that a previously unrecognized climate-related coupling may be active.

Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors

Deamination of 5-methylcytosine residues in DNA gives rise to the G/T mismatched base pair. In humans this lesion is repaired by a mismatch-specific thymine DNA glycosylase (TDG or G/T glycosylase), which catalyzes specific excision of the thymine base through N-glycosidic bond hydrolysis. Unlike other DNA glycosylases, TDG recognizes an aberrant pairing of two normal bases rather than a damaged base per se. An important structural issue is thus to understand how the enzyme specifically targets the T (or U) residue of the mismatched base pair. Our approach toward the study of substrate recognition and processing by catalytic DNA binding proteins has been to modify the substrate so as to preserve recognition of the base but to prevent its excision. Here we report that replacement of 2′-hydrogen atoms with fluorine in the substrate 2′-deoxyguridine (dU) residue abrogates glycosidic bond cleavage, thereby leading to the formation of a tight, specific glycosylase–DNA complex. Biochemical characterization of these complexes reveals that the enzyme protects an ≈20-bp stretch of the substrate from DNase I cleavage, and directly contacts a G residue on the 3′ side of the mismatched U derivative. These studies provide a mechanistic rationale for the preferential repair of deaminated CpG sites and pave the way for future high-resolution studies of TDG bound to DNA.

Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography

The positional relationships among all of the visible organelles in a densely packed region of cytoplasm from an insulin secreting, cultured mammalian cell have been analyzed in three dimensions (3-D) at ≈6 nm resolution. Part of a fast frozen/freeze-substituted HIT-T15 cell that included a large portion of the Golgi ribbon was reconstructed in 3-D by electron tomography. The reconstructed volume (3.1 × 3.2 × 1.2 μm3) allowed sites of interaction between organelles, and between microtubules and organellar membranes, to be accurately defined in 3-D and quantitatively analyzed by spatial density analyses. Our data confirm that the Golgi in an interphase mammalian cell is a single, ribbon-like organelle composed of stacks of flattened cisternae punctuated by openings of various sizes [Rambourg, A., Clermont, Y., & Hermo, L. (1979) Am. J. Anat. 154, 455–476]. The data also show that the endoplasmic reticulum (ER) is a single continuous compartment that forms close contacts with mitochondria, multiple trans Golgi cisternae, and compartments of the endo-lysosomal system. This ER traverses the Golgi ribbon from one side to the other via cisternal openings. Microtubules form close, non-random associations with the cis Golgi, the ER, and endo-lysosomal compartments. Despite the dense packing of organelles in this Golgi region, ≈66% of the reconstructed volume is calculated to represent cytoplasmic matrix. We relate the intimacy of structural associations between organelles in the Golgi region, as quantified by spatial density analyses, to biochemical mechanisms for membrane trafficking and organellar communication in mammalian cells.

Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2∷kan mutant

Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec− and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4′,6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16% of the cells were filamented and had poorly partitioned chromosomes (Par−). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par− phenotype. Filamentation in the recB mutant decreased to 3%, but increased to 28% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1∷cat was lethal with priA2∷kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.

From supervision to resolution: next steps on the road to European Banking Union. Bruegel Policy Contribution 2013/04, February 2012

The European Council has outlined the creation of a Single Resolution Mechanism (SRM), complementing the Single Supervisory Mechanism. The thinking on the SRM’s legal basis, design and mission is still preliminary and depends on other major initiatives, including the European Stability Mechanism’s involvement in bank recapitalisations and the Bank Recovery and Resolution (BRR) Directive. The SRM should also not be seen as the final step creating Europe’s future banking union. Both the BRR Directive and the SRM should be designed to enable the substantial financial participation of existing creditors in future bank restructurings. To be effective, the SRM should empower a central body. However, in the absence of Treaty change and of further fiscal integration, SRM decisions will need to be implemented through national resolution regimes. The central body of the SRM should be either the European Commission, or a new authority. This legislative effort should not be taken as an excuse to delay decisive action on the management and resolution of the current European banking fragility, which imposes a major drag on Europe’s growth and employment.

The Bank Resolution Compromise: Incomplete, but workable? CEPS Commentary, 19 December 2013

Calling the Single Resolution Mechanism an “inelegant step in the right direction”, this Commentary singles out the Single Resolution Fund, with its considerable mutualisation of risk, as the key advance – but one that will require changes over time in the extremely complex decision-making mechanisms agreed.

High-resolution dynamical downscaling products for the North Slope of Alaska and surrounding areas, links to model result files

Climatic changes are most pronounced in northern high latitude regions. Yet, there is a paucity of observational data, both spatially and temporally, such that regional-scale dynamics are not fully captured, limiting our ability to make reliable projections. In this study, a group of dynamical downscaling products were created for the period 1950 to 2100 to better understand climate change and its impacts on hydrology, permafrost, and ecosystems at a resolution suitable for northern Alaska. An ERA-interim reanalysis dataset and the Community Earth System Model (CESM) served as the forcing mechanisms in this dynamical downscaling framework, and the Weather Research & Forecast (WRF) model, embedded with an optimization for the Arctic (Polar WRF), served as the Regional Climate Model (RCM). This downscaled output consists of multiple climatic variables (precipitation, temperature, wind speed, dew point temperature, and surface air pressure) for a 10 km grid spacing at three-hour intervals. The modeling products were evaluated and calibrated using a bias-correction approach. The ERA-interim forced WRF (ERA-WRF) produced reasonable climatic variables as a result, yielding a more closely correlated temperature field than precipitation field when long-term monthly climatology was compared with its forcing and observational data. A linear scaling method then further corrected the bias, based on ERA-interim monthly climatology, and bias-corrected ERA-WRF fields were applied as a reference for calibration of both the historical and the projected CESM forced WRF (CESM-WRF) products. Biases, such as, a cold temperature bias during summer and a warm temperature bias during winter as well as a wet bias for annual precipitation that CESM holds over northern Alaska persisted in CESM-WRF runs. The linear scaling of CESM-WRF eventually produced high-resolution downscaling products for the Alaskan North Slope for hydrological and ecological research, together with the calibrated ERA-WRF run, and its capability extends far beyond that. Other climatic research has been proposed, including exploration of historical and projected climatic extreme events and their possible connections to low-frequency sea-atmospheric oscillations, as well as near-surface permafrost degradation and ice regime shifts of lakes. These dynamically downscaled, bias corrected climatic datasets provide improved spatial and temporal resolution data necessary for ongoing modeling efforts in northern Alaska focused on reconstructing and projecting hydrologic changes, ecosystem processes and responses, and permafrost thermal regimes. The dynamical downscaling methods presented in this study can also be used to create more suitable model input datasets for other sub-regions of the Arctic.

REST mediates resolution of HIF-dependent gene expression in prolonged hypoxia

The hypoxia-inducible factor (HIF) is a key regulator of the cellular response to hypoxia which promotes oxygen delivery and metabolic adaptation to oxygen deprivation. However, the degree and duration of HIF-1α expression in hypoxia must be carefully balanced within cells in order to avoid unwanted side effects associated with excessive activity. The expression of HIF-1α mRNA is suppressed in prolonged hypoxia, suggesting that the control of HIF1A gene transcription is tightly regulated by negative feedback mechanisms. Little is known about the resolution of the HIF-1α protein response and the suppression of HIF-1α mRNA in prolonged hypoxia. Here, we demonstrate that the Repressor Element 1-Silencing Transcription factor (REST) binds to the HIF-1α promoter in a hypoxia-dependent manner. Knockdown of REST using RNAi increases the expression of HIF-1α mRNA, protein and transcriptional activity. Furthermore REST knockdown increases glucose consumption and lactate production in a HIF-1α- (but not HIF-2α-) dependent manner. Finally, REST promotes the resolution of HIF-1α protein expression in prolonged hypoxia. In conclusion, we hypothesize that REST represses transcription of HIF-1α in prolonged hypoxia, thus contributing to the resolution of the HIF-1α response.

Mechanisms for triggering high-voltage breakdown in vacuum

The electrical and optical characteristics of a cylindrical alumina insulator (94% Al203) have been measured under ultra-high vacuum (P < 10-8 mBar) conditions. A high-resolution CCD camera was used to make real-time optical recordings of DC prebreakdown luminescence from the ceramic, under conditions where DC current magnitudes were limited to less than 50μA. Two concentric metallized rings formed a pair of co-axial electrodes, on the end-face of the alumina tube; a third 'transparent' electrode was employed to study the effect of an orthogonal electric field upon the radial conduction processes within the metallized alumina specimen. The wavelength-spectra of the emitted light was quantified using a high-speed scanning monochromator and photo-multiplier tube detector. Concurrent electrical measurements were made alongside the recording of optical-emission images. An observed time-dependence of the photon-emission is correlated with a time-variation observed in the DC current-voltage characteristics of the alumina. Optical images were also recorded of pulsed-field surface-flashover events on the alumina ceramic. An intensified high-speed video technique provided 1ms frames of surface-flashover events, whilst 100ns frames were achieved using an ultra high-speed fast-framing camera. By coupling this fast-frame camera to a digital storage oscilloscope, it was possible to establish a temporal correlation between the application of a voltage-pulse to the ceramic and the evolution of photonic emissions from the subsequent surface-flashover event. The electro-optical DC prebreakdown characteristics of the alumina are discussed in terms of solid-state photon-emission processes, that are believed to arise from radiative electron-recombination at vacancy-defects and substitutional impurity centres within the surface-layers of the ceramic. The physical nature of vacancy-defects within an alumina dielectric is extensively explored, with a particular focus placed upon the trapped electron energy-levels that may be present at these defect centres. Finally, consideration is given to the practical application of alumina in the trigger-ceramic of a sealed triggered vacuum gap (TVG) switch. For this purpose, a physical model describing the initiation of electrical breakdown within the TVG regime is proposed, and is based upon the explosive destabilisation of trapped charge within the alumina ceramic, triggering the onset of surface-flashover along the insulator. In the main-gap prebreakdown phase, it is suggested that the electrical-breakdown of the TVG is initiated by the low-field 'stripping' of prebreakdown electrons from vacancy-defects in the ceramic under the influence of an orthogonal main-gap electric field.

Current understanding of the mechanisms for clearance of apoptotic cells-a fine balance

Apoptosis is an important cell death mechanism by which multicellular organisms remove unwanted cells. It culminates in a rapid, controlled removal of cell corpses by neighboring or recruited viable cells. Whilst many of the molecular mechanisms that mediate corpse clearance are components of the innate immune system, clearance of apoptotic cells is an anti-inflammatory process. Control of cell death is dependent on competing pro-apoptotic and anti-apoptotic signals. Evidence now suggests a similar balance of competing signals is central to the effective removal of cells, through so called 'eat me' and 'don't eat me' signals. Competing signals are also important for the controlled recruitment of phagocytes to sites of cell death. Consequently recruitment of phagocytes to and from sites of cell death can underlie the resolution or inappropriate propagation of cell death and inflammation. This article highlights our understanding of mechanisms mediating clearance of dying cells and discusses those mechanisms controlling phagocyte migration and how inappropriate control may promote important pathologies. © the authors, publisher and licensee libertas academica limited.

High-resolution cyclostratigraphy of the Cenomanian-Turonian interval: Paleoceanographic implications, a comparison between deep sea drilling project site 386 and 144

The purpose of this study was to determine the extent to which oceanic anoxic events (OAE's) are recorded in deep-water deposits of the former western Tethyan Sea, by investigating the Cenomanian-Turonian time interval characterized by the worldwide OAE 2 event. The study improved our knowledge of the possible controlling mechanisms that triggered this event at these sites, and furthered our understanding of this global phenomenon. This was examined by high-resolution, multi-proxy analyses of sediments at DSDP Sites 386 and 144, including sedimentology, scanning electron microscopy, stable isotopes, bulk and clay mineralogy, major and trace element geochemistry, biomarkers, and paleontological data. ^ The results provide a better stratigraphic resolution for the Cenomanian-Turonian, which allowed for more precise determination of chronologic boundaries, sedimentation rates at DSDP Site 386, and a more accurate calculation of the frequency of the cycles recorded in the sequence, which fall predominantly within the precession (∼23 kyr) and short eccentricity (∼100 kyr) ranges. The combined proxies allow assessment of the correlation of δ13Corg, and major and trace elements with the predominance of cyanobacteria. These organisms were the main producers of the organic matter during the dysoxic and euxinic conditions of OAE 2 at DSDP Site 386. A huge amount of microcrystalline quartz of eolian origin is also associated with OAE 2. The geochemical proxies further provide evidence that OAE 2 was linked to increased volcanism outside the deep water of the proto-Atlantic Ocean. The clays in the Turonian sediments are terrigenous and derived predominantly from eolian transport. Comparing DSDP Site 386 and 144 with stratotype sections, the δ13C org and TOC data indicate that OAE 2 seems diachronous throughout the proto-Atlantic Ocean. ^ This study concludes that the development of anoxic conditions in the deep water of the Atlantic during the latest Cenomanian-Turonian resulted from a combination of factors related to local oceanic setting and mitigated by global tectonism and climate. The data provide a more comprehensive view of the interacting factors that led to sustained high productivity of the cyanobacteria and photosynthetic protists that produced organic-carbon-rich deposits in the world's oceans. ^

Mechanisms of chloroperoxidase-catalyzed enantioselective reactions as probed by site-directed mutagenesis and isotopic labeling

Chloroperoxidase (CPO) is a heme-containing glycoprotein secreted by the marine fungus Caldariomyces fumago. Chloroperoxidase contains one ferriprotoporphyrin IX prosthetic group per molecule and catalyzes a variety of reactions, such as halogenation, peroxidation and epoxidation. The versatile catalytic activities of CPO coupled with the increasing demands for chiral synthesis have attracted an escalating interest in understanding the mechanistic and structural properties of this enzyme. In order to better understand the mechanisms of CPO-catalyzed enantioselective reactions and to fine-tune the catalytic properties of chloroperoxidase, asparagine 74 (N74) located in the narrow substrate access channel of CPO was replaced by a bulky, nonpolar valine and a polar glutamine using site-directed mutagenesis. The CPO N74 mutants displayed significantly enhanced activity toward nonpolar substrates compared to wild-type CPO as a result of changes in space and polarity of the heme distal environment. More interestingly, N74 mutants showed dramatically decreased chlorination and catalase activity but significantly enhanced epoxidation activity as a consequence of improved kinetic perfection introduced by the mutation as reflected by the favorable changes in k cat and kcat/KM of these reactions. It is also noted that the N74V mutant is capable of decomposing cyanide, the most notorious poison for many hemoproteins, as judged by the unique binding behavior of N74V with potassium cyanide. Histidine 105 (H105) was replaced by a nonpolar amino acid alanine using site-directed mutagenesis. The CPO H105 mutant (H105A) displayed dramatically decreased chlorination and catalase activity possibly because of the decreased polarity in the heme distal environment and loss of the hydrogen bonds between histidine 105 and glutamic acid 183. However, significantly increased enantioselectivity was observed for the epoxidation of bulky styrene derivatives. Furthermore, my study provides strong evidence for the proposed histidine/cysteine ligand switch in chloroperoxidase, providing experimental support for the structure of the 420-nm absorption maximum for a number of carbon monoxide complexes of heme-thiolate proteins. For the NMR study, [dCPO(heme)] was produced using 90% deuterated growth medium with excess heme precursors and [dCPO(Phe)] was grown in the same highly deuterated medium that had been supplemented with excess natural phenylalanine. To make complete heme proton assignments, NMR spectroscopy has been performed for high-resolution structural characterization of [dCPO(heme)] and [dCPO(Phe)] to achieve unambiguous and complete heme proton assignments, which also allows important amino acids close to the heme active center to be determined.

High resolution numerical simulation of triple point collision and origin of unburned gas pockets in turbulent detonations

A key issue in pulse detonation engine development is better understanding of the detonation structure and its propagation mechanism. Thus, in the present work the turbulent structure of an irregular detonation is studied through very high resolution numerical simulations of 600 points per half reaction length. The aim is to explore the nature of the transverse waves during the collision and reflection processes of the triple point with the channel walls. Consequently the formation and consumption mechanism of unreacted gas pockets is studied. Results show that the triple point and the transverse wave collide simultaneously with the wall. The strong transverse wave switches from a primary triple point before collision to a new one after reflection. Due to simultaneous interaction of the triple point and the transverse wave with the wall in the second half of the detonation cell, a larger high-pressurised region appears on the wall. During the reflection the reaction zone detaches from the shock front and produces a pocket of unburned gas. Three mechanisms found to be of significance in the re-initiation mechanism of detonation at the end of the detonation cell; i: energy resealed via consumption of unburned pockets by turbulent mixing ii: compression waves arise due to collision of the triple point on the wall which helps the shock to jump abruptly to an overdriven detonation iii: drastic growth of the Richtmyer–Meshkov instability causing a part of the front to accelerate with respect to the neighbouring portions.