Structural model of the CopA copper ATPase of Enterococcus hirae based on chemical cross-linking

The CopA copper ATPase of Enterococcus hirae belongs to the family of heavy metal pumping CPx-type ATPases and shares 43% sequence similarity with the human Menkes and Wilson copper ATPases. Due to a lack of suitable protein crystals, only partial three-dimensional structures have so far been obtained for this family of ion pumps. We present a structural model of CopA derived by combining topological information obtained by intramolecular cross-linking with molecular modeling. Purified CopA was cross-linked with different bivalent reagents, followed by tryptic digestion and identification of cross-linked peptides by mass spectrometry. The structural proximity of tryptic fragments provided information about the structural arrangement of the hydrophilic protein domains, which was integrated into a three-dimensional model of CopA. Comparative modeling of CopA was guided by the sequence similarity to the calcium ATPase of the sarcoplasmic reticulum, Serca1, for which detailed structures are available. In addition, known partial structures of CPx-ATPase homologous to CopA were used as modeling templates. A docking approach was used to predict the orientation of the heavy metal binding domain of CopA relative to the core structure, which was verified by distance constraints derived from cross-links. The overall structural model of CopA resembles the Serca1 structure, but reveals distinctive features of CPx-type ATPases. A prominent feature is the positioning of the heavy metal binding domain. It features an orientation of the Cu binding ligands which is appropriate for the interaction with Cu-loaded metallochaperones in solution. Moreover, a novel model of the architecture of the intramembranous Cu binding sites could be derive

Global forestation and deforestation affect remote climate via adjusted atmosphere and ocean circulation.

Forests can store large amounts of carbon and provide essential ecosystem services. Massive tree planting is thus sometimes portrayed as a panacea to mitigate climate change and related impacts. Recent controversies about the potential benefits and drawbacks of forestation have centered on the carbon storage potential of forests and the local or global thermodynamic impacts. Here we discuss how global-scale forestation and deforestation change the Earth's energy balance, thereby affect the global atmospheric circulation and even have profound effects on the ocean circulation. We perform multicentury coupled climate model simulations in which preindustrial vegetation cover is either completely forested or deforested and carbon dioxide mixing ratio is kept constant. We show that global-scale forestation leads to a weakening and poleward shift of the Northern mid-latitude circulation, slows-down the Atlantic meridional overturning circulation, and affects the strength of the Hadley cell, whereas deforestation leads to reversed changes. Consequently, both land surface changes substantially affect regional precipitation, temperature, clouds, and surface wind patterns across the globe. The design process of large-scale forestation projects thus needs to take into account global circulation adjustments and their influence on remote climate

Non-repudiable authentication and billing architecture for wireless mesh networks

The original publication is available at www.springerlink.comWireless mesh networks (WMNs) are a kind of wireless ad hoc networks that are multi-hop where packets are forwarded from source to destination by intermediate notes as well as routers that form a kind of network infrastructure backbone. We investigate the security of the recently proposed first known secure authentication and billing architecture for WMNs which eliminates the need for bilateral roaming agreements and that for traditional home-foreign domains. We show that this architecture does not securely provide incontestable billing contrary to designer claims and furthermore it does not achieve entity authentication. We then present an enhanced scheme that achieves entity authentication and nonrepudiable billing

The life cycles of potential vorticity cutoffs: climatology, predictability and high impact weather

Stratospheric potential vorticity (PV) cutoffs are ubiquitous synoptic- to meso-scale cyclonic vortices at upper-tropospheric levels that occur frequently from subtropical to polar latitudes. PV cutoffs are usually identified as quasi-circular regions of stratospheric air isolated from the main stratospheric reservoir on an isentropic surface. Their genesis is the result of breaking synoptic-scale Rossby waves and their life cycle ends either via decay by diabatic processes or via advection back to the stratospheric reservoir (in this thesis referred to as `reabsorption'). PV cutoffs have been in the focus of dynamical meteorologists for more than 70 years mainly because of two reasons: (i) They frequently result in high impact surface weather, in particular heavy precipitation, and (ii) their decay due to diabatic processes results in the transport of stratospheric air masses into the troposphere and thereby affects the concentration of trace gases (e.g. water vapour, ozone) in the atmosphere. While many case studies of PV cutoffs exist and their climatological frequencies are well known, various climatological aspects of their life cycle and their surface impacts are still poorly understood. Also, a comprehensive global analysis of PV cutoffs is yet missing. However, this not only required in order to better assess their fundamental role for various aspects of the atmospheric circulation and chemistry (e.g. for cyclogenesis, the transport of moisture and aerosols, mixing of stratospheric ozone into the troposphere), but also to quantify their relevance for (high impact) surface weather in current and future climates. Current understanding of the relevance of PV cutoffs for high impact weather implies that their accurate prediction by state-of-the-art operational forecasting systems is essential to avoid socio-economic harm. However, only few case studies have investigated forecast uncertainties related to PV cutoffs. In summary, these studies pointed at three key aspects: (i) the direct effect of uncertainties related to PV cutoffs for surface weather, (ii) the role of upstream processes for uncertainties in the formation of PV cutoffs downstream, such as the extratropical transition of tropical cyclones and warm conveyor belts (WCBs), and (iii) the role of PV cutoff reabsorption for downstream uncertainties in the wave guide. The relevance of these aspects have not yet been addressed systematically and only little is known about the dynamics governing the propagation of uncertainties in these situations.\\ This thesis consist of two parts. The first part addresses various climatological aspects of the life cycle of PV cutoffs as well as their contribution to (extreme) precipitation and the second part focuses on forecast uncertainties related to PV cutoffs. To study the life cycle of PV cutoffs, a novel method is introduced to track PV cutoffs as three-dimensional objects. As this method is based on isentropic trajectories, cross-tropopause mass fluxes can also be quantified. Its application to 39 years of the ECMWF reanalysis dataset leads to the first global climatology of PV cutoffs that is independent of the selection of a single vertical level. In addition to known geographical frequency maxima, large regions over subtropical ocean basins in the summer hemispheres and a circumpolar band around Antarctica are identified. The three-dimensional life cycles of more than 40'000 PV cutoffs are identified and analyzed in detail, including their link to surface cyclones. Remarkable regional differences are found which provide the basis for a new classification of PV cutoff life cycles into three types (Types I, II, and III). Type I PV cutoffs form mostly in summer over subtropical ocean basins as a result of anticyclonic Rossby wave breaking equatorward of the jet stream. They can be relatively stationary and long lived, can grow downward in their vertical extent, and are only rarely connected to surface cyclones. Their life cycle ends mostly with diabatic decay. Type II PV cutoffs form from anticyclonic followed by cyclonic Rossby wave breaking between the polar and the subtropical jets. Their formation often occurs simultaneously with surface cyclogenesis and strong diabatic activity results in rapid decay at lower isentropic levels. At the end of their life cycle, diabatic decay and reabsorption are equally likely. Finally, Type III PV cutoffs form poleward of the jet stream by cyclonic Rossby wave breaking in the storm track regions. Typically, they are associated to surface cyclones that formed a few days earlier and their evolution is often rather adiabatic, i.e. without frequent diabatic decay and vertical displacement. Their life cycle ends most frequently with reabsorption. This dataset of PV cutoffs is used to attribute (extreme) precipitation to PV cutoffs and study the evolution of precipitation along their life cycle. It is found that Type I PV cutoffs often result in only little precipitation while Type II and III PV cutoffs are frequently accompanied by high precipitation volumes. Further, we find that enhanced meridional moisture transport is crucial for large precipitation amounts related to PV cutoffs. The first global quantification of the contribution of PV cutoffs to average and extreme precipitation reveals that PV cutoffs are particularly relevant in semi-arid subtropical regions (so-called Mediterranean climate regions), which are in fact the regions that are expected to experience the strongest changes in the hydrological cycle due to anthropogenic climate change. The second part of the thesis contains two separate studies, which are both based on ECMWF operational ensemble forecasts and analyses. First, a detailed case study shows how forecast uncertainty can propagate from the North Atlantic along the wave guide into the Mediterranean and lead to an uncertain PV cutoff genesis position and, as a result, an uncertain development of an intense Mediterranean tropical-like cyclone (medicane). In particular, it is highlighted, that the uncertainties initially emerge from a North Atlantic jet streak and propagate and amplify into the Mediterranean during Rossby wave breaking. Further, it shows how uncertainties in the PV cutoff genesis position substantially affect the vertical thermal structure of the Mediterranean cyclone. These results contribute to improved understanding of the predictability of PV cutoffs and medicanes. The second study aims to investigate more systematically how PV cutoffs affect forecast uncertainties. It is shown that PV cutoff genesis over the Mediterranean is systematically accompanied by enhanced forecast uncertainty which is largest at genesis time. PV cutoff reabsorption, however, does not show a systematic signal in the region considered and with the method used. Further, a systematic link between strong North Atlantic WCBs and forecast uncertainty in both, the North Atlantic region and the Mediterranean is found. This link is particularly strong for the Mediterranean where the effect of strong North Atlantic WCBs is twofold: First, WCBs introduce (or amplify pre-existing) forecast uncertainties in the North Atlantic wave guide and second, they support the establishment of large-scale conditions that direct the North Atlantic jet stream towards the Mediterranean, which provides a corridor for the propagation of forecast uncertainties. Overall, this thesis provides new perspectives on the life cycle of PV cutoffs. It proposes a new classification of PV cutoffs which stresses the regional variability of their genesis and lysis dynamics, their vertical evolution, and surface impacts. Furthermore, it points out the relevance of PV cutoffs for (extreme) precipitation, especially in Mediterranean climate regions. On the other hand, this work offers new insight into the origin and dynamics of medium-range forecast uncertainty for the North Atlantic and Mediterranean regions in general, and, more specifically, for PV cutoffs. The thesis points out the relevance of strong North Atlantic WCBs for enhanced forecast uncertainty and demonstrates the tight link between forecast uncertainties over the North Atlantic and the Mediterranean under suitable conditions. The results imply that the uncertainties associated to PV cutoffs, e.g. in their position or intensity, often originate from upstream processes and are handed over to PV cutoffs during Rossby wave breaking. PV cutoffs subsequently transfer these uncertainties to (high impact) surface weather. Hence, with this work we underline that PV cutoffs are highly relevant flow features that contribute substantially to the complex dynamics of the extratropical circulation, to high impact weather and its predictability, as well as the hydrology of Mediterranean climate regions

The three-dimensional life cycles of potential vorticity cutoffs: a global and selected regional climatologies in ERA-Interim (1979–2018)

The aim of this study is to explore the nature of potential vorticity (PV) cutoff life cycles. While climatological frequencies of such near-tropopause cyclonic vortices are well known, their life cycle and in particular their three-dimensional evolution is poorly understood. To address this gap, a novel method is introduced that uses isentropic air parcel trajectories to track PV cutoffs as three-dimensional objects. With this method, we can distinguish the two fundamentally different PV cutoff lysis scenarios on isentropic surfaces: complete diabatic decay vs. reabsorption by the stratospheric reservoir. This method is applied to the ERA-Interim dataset (1979–2018), and the first global climatology of PV cutoffs is presented that is independent of the selection of a vertical level and identifies and tracks PV cutoffs as three-dimensional features. More than 150 000 PV cutoff life cycles are identified and analyzed. The climatology confirms known frequency maxima of PV cutoffs and identifies additional bands in subtropical areas in the summer hemispheres and a circumpolar band around Antarctica. The first climatological analysis of diabatic decay and reabsorption shows that both scenarios occur equally frequently – in contrast to the prevailing opinion that diabatic decay dominates. Then, PV cutoffs are classified according to their position relative to jet streams (equatorward (Type I), between two jets (Type II), and poleward (Type III)). A composite analysis shows distinct dynamical scenarios for the genesis of the three types. Type I forms due to anticyclonic Rossby wave breaking above subtropical surface anticyclones and hardly results in precipitation. Type II results from anticyclonic Rossby wave breaking in mid-latitudes in regions with split-jet conditions and is frequently accompanied by surface cyclogenesis and substantial precipitation. Type III cutoffs preferentially form due to cyclonic Rossby wave breaking within extratropical cyclones in the storm track regions. We show that important track characteristics (speed, travel distance, frequency of decay and reabsorption, isentropic levels) differ between the categories, while lifetime is similar in all categories. Finally, 12 PV cutoff genesis regions in DJF and JJA are selected to study the regional characteristics of PV cutoff life cycles. As a particularly novel aspect, the vertical evolution of PV cutoffs along the life cycle is investigated. We find that, climatologically, PV cutoffs reach their maximum vertical extent about one day after genesis in most regions. However, while in some regions PV cutoffs rapidly disappear at lower levels by diabatic decay, they can grow downward in other regions. In addition, regional differences in lifetimes, the frequencies of diabatic decay and reabsorption, and the link to surface cyclones are identified that cannot be explained only by the preferred regional occurrence of the different cutoff types as defined above. Finally, we also show that in many regions PV cutoffs can be involved in surface cyclogenesis even after their formation. This study is an important step towards quantifying fundamental dynamical characteristics and the surface impacts of PV cutoffs. The proposed classification according to the jet-relative position provides a useful way to improve the conceptual understanding of PV cutoff life cycles in different regions of the globe. However, these life cycles can be substantially modified by specific regional conditions.ISSN:2698-4016ISSN:2698-400

The complex life cycles of two long-lived potential vorticity cut-offs over Europe

ISSN:0035-9009ISSN:1477-870

The role of cyclones and potential vorticity cutoffs for the occurrence of unusually long wet spells in Europe

The synoptic dynamics leading to the longest wet spells in Europe are so far poorly investigated despite these events' potentially large societal impacts. Here we examine the role of cyclones and potential vorticity (PV) cutoffs for unusually long wet spells in Europe, defined as the 20 longest uninterrupted periods with at least 5 mm daily accumulated precipitation at each ERA-Interim grid point in Europe (this set of spells is hereafter referred to as S20). The S20 occur predominantly in summer over the eastern continent, in winter over the North Atlantic, in winter or fall over the Atlantic coast, and in fall over the Mediterranean and European inland seas. Four case studies reveal distinct archetypal synoptic storylines for long wet spells: (a) a 7 d wet spell near Moscow, Russia, is associated with a single slow-moving cutoff-cyclone couple; (b) a 15 d wet spell in Norway features a total of nine rapidly passing extratropical cyclones and illustrates serial cyclone clustering as a second storyline; (c) a 12 d wet spell in Tuscany, Italy, is associated with a single but very large cutoff complex, which is replenished multiple times by a sequence of recurrent anticyclonic wave breaking events over the North Atlantic and western Europe; and (d) a 17 d wet spell in the Balkans features intermittent periods of diurnal convection in an environment of weak synoptic forcing and recurrent passages of cutoffs and thus also highlights the role of diurnal convection for long wet spells over land. A systematic analysis of cyclone and cutoff occurrences during the S20 across Europe reveals considerable spatial variability in their respective role for the S20. For instance, cyclones are present anywhere between 10 % and 90 % and cutoffs between 20 % and 70 % of the S20 time steps, depending on the geographical region. However, overall both cyclones and cutoffs appear in a larger number and at a higher rate during the S20 compared to climatology. Furthermore, in the Mediterranean, cutoffs and cyclones are significantly more persistent during the S20 compared to climatology. Our study thus documents for the first time the palette of synoptic storylines accompanying unusually long wet spells across Europe, which is a prerequisite for developing an understanding of how these events might change in a warming climate and for evaluating the ability of climate models to realistically simulate the synoptic processes relevant to these events.ISSN:2698-4016ISSN:2698-400

How an uncertain short-wave perturbation on the North Atlantic wave guide affects the forecast of an intense Mediterranean cyclone (Medicane Zorbas)

Mediterranean cyclogenesis is known to be frequently linked to ridge building over the North Atlantic and subsequent anticyclonic Rossby wave breaking over Europe. But understanding of how this linkage affects the medium-range forecast uncertainty of Mediterranean cyclones is limited, as previous predictability studies have mainly focused on the relatively rare cases of Mediterranean cyclogenesis preceded by upstream extratropical transition of tropical cyclones. This study exploits a European Centre for Medium-Range Weather Forecasts (ECMWF) operational ensemble forecast with an uncertain potential vorticity (PV) streamer position over the Mediterranean that, 3 d after initialization, resulted in an uncertain development of the Mediterranean tropical-like cyclone (Medicane) Zorbas in September 2018. Later initializations showed substantially lower forecast uncertainties over the Mediterranean. An ad hoc clustering of the ensemble members according to the PV streamer position in the Mediterranean is used to study the upstream evolution of the synoptic to mesoscale forecast uncertainties. Cluster differences show that forecast uncertainties were amplified on the stratospheric side of a jet streak over the North Atlantic during the first day of the ensemble prediction. Subsequently, they propagated downstream and were further amplified within a short-wave perturbation along the wave guide, superimposed onto the large-scale Rossby wave pattern. After 3 d, the uncertainties reached the Mediterranean, where they resulted in a large spread in the position of the PV streamer. These uncertainties further translated into uncertainties in the position and thermal structure of the Mediterranean cyclone. In particular, the eastward displacement of the PV streamer in more than a third of the ensemble members resulted in a very different cyclone scenario. In this scenario, cyclogenesis occurred earlier than in the other members in connection to a pre-existing surface trough over the Levantine Sea. These cyclones did not develop the deep warm core typical of medicanes. It is proposed that the eastward-shifted cyclogenesis resulted in reduced values of low-level equivalent potential temperature in the cyclogenesis area. As a result, latent heating was not intense and deep enough to erode the upper-level PV anomaly and allow the formation of a deep warm core. The westward displacement led to surface cyclones that were too weak, and a medicane formed in only half of the members. The central, i.e. correct, PV streamer position resulted in the most accurate forecasts with a strong medicane in most members. This study is the first that explicitly investigates the impact of PV streamer position uncertainty for medicane development. Overall, results extend current knowledge of the role of upstream uncertainties in the medium-range predictability and unsteady forecast behavior of Mediterranean cyclones including medicanes.ISSN:2698-4016ISSN:2698-400

Modelling crop hail damage footprints with single-polarization radar: the roles of spatial resolution, hail intensity, and cropland density

<jats:p>Abstract. Hail represents a major threat to agriculture in Switzerland, and assessments of current and future hail risk are of paramount importance for decision-making in the insurance industry and the agricultural sector. However, relating observational information on hail with crop-specific damage is challenging. Here, we build and systematically assess an open-source model to predict hail damage footprints for field crops (wheat, maize, barley, rapeseed) and grapevine from the operational radar product Maximum Expected Severe Hail Size (MESHS) at different spatial resolutions. To this end, we combine the radar information with detailed geospatial information on agricultural land use and geo-referenced damage data from a crop insurer for 12 recent hail events in Switzerland. We find that for field crops model skill gradually increases when the spatial resolution is reduced from 1 km down to 8 km. For even lower resolutions, the skill is diminished again. In contrast, for grapevine, decreasing model resolution below 1 km tends to reduce skill, which is attributed to the different spatial distribution of field crops and grapevine in the landscape. It is shown that identifying a suitable MESHS thresholds to model damage footprints always involves trade-offs. For the lowest possible MESHS threshold (20 mm) the model predicts damage about twice as often as observed (high frequency bias and false alarm ratio), but it also has a high probability of detection (80 %). The frequency bias decreases for larger thresholds and reaches an optimal value close to 1 for MESHS thresholds of 30–40 mm. However, this comes at the cost of a substantially lower probability of detection (around 50 %), while overall model skill, as measured by the Heidke skill score (HSS), remains largely unchanged (0.41–0.44). We argue that, ultimately, the best threshold therefore depends on the relative costs of a false alarm versus a missed event. Finally, the frequency of false alarms is substantially reduced and skill is improved (HSS = 0.54) when only areas with high cropland density are considered. Results from this simple, open-source model show that modelling of hail damage footprints to crops from single-polarization radar in Switzerland is skilful and is best done at 8 km resolution for field crops and 1 km for grapevine. </jats:p&gt