Tolerance of Arc repressor to multiple-alanine substitutions

Arc repressor mutants containing from three to 15 multiple-alanine substitutions have spectral properties expected for native Arc proteins, form heterodimers with wild-type Arc, denature cooperatively with Tms equal to or greater than wild type, and, in some cases, fold as much as 30-fold faster and unfold as much as 50-fold slower than wild type. Two of the mutants, containing a total of 14 different substitutions, also footprint operator DNA in vitro. The stability of some of the proteins with multiple-alanine mutations is significantly greater than that predicted from the sum of the single substitutions, suggesting that a subset of the wild-type residues in Arc may interact in an unfavorable fashion. Overall, these results show that almost half of the residues in Arc can be replaced by alanine en masse without compromising the ability of this small, homodimeric protein to fold into a stable, native-like structure.

Dual regulation of open-complex formation and promoter clearance by Arc explains a novel repressor to activator switch.

In studies of variants of the P(ant) promoter of bacteriophage P22, the Arc protein was found not only to slow the rate at which RNA polymerase forms open complexes but also to accelerate the rate at which the enzyme clears the promoter. These dual activities permit Arc, bound at a single operator subsite, to act as an activator or as a repressor of different promoter variants. For example, Arc activates a P(ant) variant for which promoter clearance is rate limiting in the presence and absence of Arc but represses a closely related variant for which open-complex formation becomes rate limiting in the presence of Arc. The acceleration of promoter clearance by Arc requires occupancy of the operator subsite proximal to the -35 region and is diminished when Arc bears a mutation in Arg-23, a residue that makes a DNA-backbone contact in the operator complex.

Evaluation of the multi-element capabilities of collision/reaction cell inductively coupled plasma - mass spectrometry in wine analysis

This work explores the multi-element capabilities of inductively coupled plasma - mass spectrometry with collision/reaction cell technology (CCT-ICP-MS) for the simultaneous determination of both spectrally interfered and non-interfered nuclides in wine samples using a single set of experimental conditions. The influence of the cell gas type (i.e. He, He+H2 and He+NH3), cell gas flow rate and sample pre-treatment (i.e. water dilution or acid digestion) on the background-equivalent concentration (BEC) of several nuclides covering the mass range from 7 to 238 u has been studied. Results obtained in this work show that, operating the collision/reaction cell with a compromise cell gas flow rate (i.e. 4 mL min−1) improves BEC values for interfered nuclides without a significant effect on the BECs for non-interfered nuclides, with the exception of the light elements Li and Be. Among the different cell gas mixtures tested, the use of He or He+H2 is preferred over He+NH3 because NH3 generates new spectral interferences. No significant influence of the sample pre-treatment methodology (i.e. dilution or digestion) on the multi-element capabilities of CCT-ICP-MS in the context of simultaneous analysis of interfered and non-interfered nuclides was observed. Nonetheless, sample dilution should be kept at minimum to ensure that light nuclides (e.g. Li and Be) could be quantified in wine. Finally, a direct 5-fold aqueous dilution is recommended for the simultaneous trace and ultra-trace determination of spectrally interfered and non-interfered elements in wine by means of CCT-ICP-MS. The use of the CCT is mandatory for interference-free ultra-trace determination of Ti and Cr. Only Be could not be determined when using the CCT due to a deteriorated limit of detection when compared to conventional ICP-MS.

A check list of mammals of the North American continent, the West Indies and the neighboring seas.

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Net Neutrality and Mandatory Network-Sharing: How to disconnect the continent. CEPS Policy Brief No. 309, 18 December 2013

A lively debate emerged on the proposed “Connected Continent” legislative package presented by the European Commission in September 2013. The package contains a proposed rule on the ‘open Internet’, which was heavily discussed in European Parliament hearings in early December. This commentary argues that while the proposed rule is in principle balanced and appealing, it is utterly impractical due to the enormous uncertainty that its application would entail. At the same time, the rule is very far from what neutrality proponents have argued for almost a decade: rather than the place for internet freedom, it would transform the Web into a place requiring constant micro-management and tutoring of user behaviour. Both arguments lead to the conclusion that the current proposal should be at once reformed and analysed under a more holistic lens. On the one hand, Europe should launch an ambitious project for the future, converged infrastructure by mobilising resources and reforming rules to encourage investment into ubiquitous, converged, ‘always on’ connectivity. On the other hand, enhanced legal certainty for broadband investment could justify a more neutrality-oriented approach to traffic management practices on the Internet. The author proposes a new approach to Internet regulation which, altogether, will lead to a more balanced and sustainable model for the future, without jeopardising user freedom.

The Re-emergence of Russia and its Collision Course with Europe. Jean Monnet/Robert Schuman Paper Series Vol. 14 No. 4, March 2014

From the Introduction. In order to understand the historical roots of the current geopolitical confrontation between the EU and Russia, we have to go back to the end of the Cold War and to the catastrophic decade that it was followed by in Russian history. The dissolution of the USSR imposed serious economic hardship for Russia and for all the ex-communist East-European states. Russia was the hardest hit amongst them, as the center of the USSR's economic system it suffered most from the dissolution of regional economic ties. This crisis was just deepened by the IMF's privatization and reform campaign, which imposed austerity measures and state-asset privatization as a “shock-therapy” answer to the country's economic problems. This policy package did nothing to save Russia from economic collapse (which eventually happened in 1998), the only thing it achieved was an even stronger social and economic crisis and the enrichment of the rent-seeking ex-communist top bureaucrats by state-assets, which were sold out under-priced through diverse channels of corruption

Prospects for Security on the European Continent. EU Diplomacy Paper 05/2015.

This collective EU Diplomacy Paper on relations between the North Atlantic Treaty Organisation (NATO) and the European Union (EU) consists of essays written by students of the EU International Relations and Diplomacy Studies programme at the College of Europe in the class on EU-NATO relations taught by Fulbright Professor Mark Sheetz in the academic year 2014-15. It seeks to provide a blueprint of what the near future of the transatlantic alliance and of the European security framework might look like. Special attention will be given to the possible effects of Finland joining NATO, Swedish-NATO relations, the question whether NATO should continue to exist at all, and finally the use of the Common Foreign and Security Policy (CFSP) and the Common Security and Defence Policy (CSDP) in relation with the transatlantic military alliance.

Nagorno-Karabakh and the arc of crises on Europe's borders. EPC Policy Brief, 3 February 2016

For more than two decades, Azerbaijan and Armenia have been locked in a stalemate over the Nagorno-Karabakh. The protracted conflict remains the biggest impediment to security, stability and prosperity in the South Caucasus. The EU has put itself on the sidelines of the conflict resolution process, allowing the Organization for Security and Co-operation in Europe (OSCE) Minsk Group (MG), of which Russia, France and the US are co-chairs, to take centre stage. In this Policy Brief, Amanda Paul and Dennis Sammut argue that the EU should play a more active role in the conflict resolution process, taking the lead with innovative initiatives and using its soft power skills and experience. A recent review of the European Neighbourhood Policy recognises that protracted conflicts continue to hamper development in the region. This new approach now needs to be given substance, before the conflict further escalates and becomes another crisis on Europe’s border the already burdened Union cannot cope with.

Structural features in ODP Holes 128-794D and 128-799B

Numerous structural features occur in the Leg 128 cores from the Japan Sea. They include (1) gravity-induced structures such as slump folds, (2) dewatering structures comprising several sets of veins, and (3) larger faults and veins developed in the volcanic basement of the Yamato Basin as well as in the sedimentary rocks of the Oki Ridge and Kita-Yamato Trough. Gravity-induced structures, mainly slumps and associated faults, suggest the existence of paleoslopes and the dominance of gravitational tectonics during the early and middle Miocene, at the Pliocene/Pleistocene boundary, and during the Quaternary. Several types of mud-filled veins having various shapes were observed. These are especially abundant in the middle Miocene siliceous claystones and porcellanites from the Kita-Yamato Trough. They have been interpreted as dewatering conduits that formed preferentially in highly porous, water-saturated diatomaceous muds on a slope, because of episodic loss of sediment strength, collapse of the sediment framework, and consequent fluid migration. The central part of the vein serves once as a fluid conduit, whereas the transition between conduit-controlled and intergranular flow occurs at the branching extremities, with concentration of fines. The likely trigger responsible for the strength loss is seismic activity. Development of these veins, spatially and chronologically linked to small normal microfaults, implies an extensional regime having layer-parallel extension and a local bedding-parallel shear couple, probably the result of gravitational gliding. The brittle fractures found in Yamato Basin basement Hole 794D cores comprise joints, faults, and veins filled with chlorite-saponite, saponite, and calcite. They suggest a likely transpressive to transtensional regime around the early Miocene/ middle Miocene boundary, with a north-northeast-south-southwest compression alternating with a west-northwest-eastsoutheast extension. The faults from Site 799 cores on the Yamato Rise exhibit a prominent early Miocene-middle Miocene extensional environment, a late Miocene-early Pliocene phase of normal and strike-slip faulting, and a final phase that began during the latest Pliocene. Site 798, on the Oki Ridge, reveals faults that recorded a consistent extensional tectonic regime from Pliocene to the Holocene. These data support the pull-apart kinematic model for early Miocene-middle Miocene time, as regarding the stress regime deduced from the Yamato Basin basement fractures. The recent compression known in the eastern margin of the Japan Sea was not documented by compressive structures at any site. The late Miocene-early Pliocene faulting phase corresponds to a major and general reorganization of the stress distribution in the arc area. Evidence for rapid and main subsidence and synsedimentary extension of the Yamato Basin and Yamato Rise areas between 20 and 15 Ma, and the concomitant rotation of southwest Japan, raise the question of links between this opening and the Shimanto Belt collision in southwest Japan, between the arc and the Philippine Sea Plate.

Greenland and Antarctic ice sheet topography, cavity geometry, and global bathymetry (RTopo-2), links to NetCDF files

The ocean plays an important role in modulating the mass balance of the polar ice sheets by interacting with the ice shelves in Antarctica and with the marine-terminating outlet glaciers in Greenland. Given that the flux of warm water onto the continental shelf and into the sub-ice cavities is steered by complex bathymetry, a detailed topography data set is an essential ingredient for models that address ice-ocean interaction. We followed the spirit of the global RTopo-1 data set and compiled consistent maps of global ocean bathymetry, upper and lower ice surface topographies and global surface height on a spherical grid with now 30-arc seconds resolution. We used the General Bathymetric Chart of the Oceans (GEBCO, 2014) as the backbone and added the International Bathymetric Chart of the Arctic Ocean version 3 (IBCAOv3) and the Interna- tional Bathymetric Chart of the Southern Ocean (IBCSO) version 1. While RTopo-1 primarily aimed at a good and consistent representation of the Antarctic ice sheet, ice shelves and sub-ice cavities, RTopo-2 now also contains ice topographies of the Greenland ice sheet and outlet glaciers. In particular, we aimed at a good representation of the fjord and shelf bathymetry sur- rounding the Greenland continent. We corrected data from earlier gridded products in the areas of Petermann Glacier, Hagen Bræ and Sermilik Fjord assuming that sub-ice and fjord bathymetries roughly follow plausible Last Glacial Maximum ice flow patterns. For the continental shelf off northeast Greenland and the floating ice tongue of Nioghalvfjerdsfjorden Glacier at about 79°N, we incorporated a high-resolution digital bathymetry model considering original multibeam survey data for the region. Radar data for surface topographies of the floating ice tongues of Nioghalvfjerdsfjorden Glacier and Zachariæ Isstrøm have been obtained from the data centers of Technical University of Denmark (DTU), Operation Icebridge (NASA/NSF) and Alfred Wegener Institute (AWI). For the Antarctic ice sheet/ice shelves, RTopo-2 largely relies on the Bedmap-2 product but applies corrections for the geometry of Getz, Abbot and Fimbul ice shelf cavities.

Element analyses and isotopic composition of basalts from the western Pacific

New Sr- Nd- and Pb-isotopic and trace element data are presented on basalts from the Sulu and Celebes Basins, and the submerged Cagayan Ridge Arc (Western Pacific), recently sampled during Ocean Drilling Program Leg 124. Drilling has shown that the Sulu Basin developed about 18 Ma ago as a backarc basin, associated with the now submerged Cagayan Ridge Arc, whereas the Celebes Basin was generated about 43 Ma ago, contemporaneous with a general plate reorganisation in the Western Pacifc, subsequently developing as an open ocean receiving pelagic sediments until the middle Miocene. In both basins, a late middle Miocene collision phase and the onset of volcanic activity on adjacent arcs in the late Miocene are recorded. Covariations between 87Sr/86Sr and 143Nd/144Nd show that the seafoor basalts from both the Sulu and Celebes Basins are isotopically similar to depleted Indian mid-ocean ridge basalts (MORB), and distinct from East Pacifc Rise MORB, defining a single negative correlation. The Cagayan Arc volcanics are different, in that they have distinctly lower epsilon-Ne(T) for a given epsilon-Sr(T), compared to Sulu and Celebes basalts. In the 207Pb/204Pb and 208Pb/204Pb versus 206Pb/204Pb diagrams, the Celebes, Sulu and Cagayan rocks all plot distinctly above the Northern Hemisphere Reference Line, with high Delta 7/4 Pb (5.3-9.3) and Delta 8/4 Pb (46.3-68.1) values. They define a single trend of radiogenic lead enrichment from Celebes through Sulu to Cagayan Ridge, within the Indian Ocean MORB data field. The data suggest that the overall chemical and isotopic features of the Sulu, Cagayan and Celebes rocks may be explained by partial melting of a depleted asthenospheric N-MORB-type ("normal") mantle source with isotopic characteristics similar to those of the Indian Ocean MORB source. This asthenospheric source was slightly heterogeneous, giving rise to the Sr-Nd isotopic differences between the Celebes and Sulu basalts, and the Cagayan Ridge volcanics. In addition, a probably slab-derived component enriched in LILE and LREE is required to generate the elemental characteristics and low Ne(T) of the Cagayan Ridge island arc tholeiitic and calcalkaline lavas, and to contribute to a small extent in the backarc basalts of the Sulu Sea. The results of this study confirm and extend the widespread Indian Ocean MORB signature in the Western Pacifc region. This signature could have been inherited by the Indian Ocean mantle itself during the rupture of Gondwanaland, when fragments of this mantle could have migrated towards the present position of the Celebes, Sulu and Cagayan sources.