Optimizing I/O forwarding techniques for extreme-scale event tracing

Programming development tools are a vital component for understanding the behavior of parallel applications. Event tracing is a principal ingredient to these tools, but new and serious challenges place event tracing at risk on extreme-scale machines. As the quantity of captured events increases with concurrency, the additional data can overload the parallel file system and perturb the application being observed. In this work we present a solution for event tracing on extreme-scale machines. We enhance an I/O forwarding software layer to aggregate and reorganize log data prior to writing to the storage system, significantly reducing the burden on the underlying file system. Furthermore, we introduce a sophisticated write buffering capability to limit the impact. To validate the approach, we employ the Vampir tracing toolset using these new capabilities. Our results demonstrate that the approach increases the maximum traced application size by a factor of 5× to more than 200,000 processes.     

Glu-333 of Nicastrin Directly Participates in ��-Secretase Activity

γ-Secretase is a proteolytic membrane complex that processes a variety of substrates including the amyloid precursor protein and the Notch receptor. Earlier we showed that one of the components of this complex, nicastrin (NCT), functions as a receptor for γ-secretase substrates. A recent report challenged this, arguing instead that the Glu-333 residue of NCT predicted to participate in substrate recognition only participates in γ-secretase complex maturation and not in activity per se. Here, we present evidence that Glu-333 directly participates in γ-secretase activity. By normalizing to the active pool of γ-secretase with two separate methods, we establish that γ-secretase complexes containing NCT-E333A are indeed deficient in intrinsic activity. We also demonstrate that the NCT-E333A mutant is deficient in its binding to substrates. Moreover, we find that the cleavage of substrates by γ-secretase activity requires a free N-terminal amine but no minimal length of the extracellular N-terminal stub. Taken together, these studies provide further evidence supporting the role of NCT in substrate recognition. Finally, because γ-secretase cleaves itself during its maturation and because NCT-E333A also shows defects in γ-secretase complex maturation, we present a model whereby Glu-333 can serve a dual role via similar mechanisms in the recruitment of both Type 1 membrane proteins for activity and the presenilin intracellular loop during complex maturation.The brains of Alzheimer disease patients are characterized by dense neuritic plaques that consist of the insoluble β-amyloid peptide (Aβ)² and neurons containing neurofibrillary tangles of the Tau protein (1, 2). The Aβ peptide is produced via the sequential proteolysis of APP by β- and γ-secretase (3). γ-secretase is a multisubunit complex consisting of at least four proteins: presenilin (PS), NCT, APH-1, and PEN-2, all of which are necessary and sufficient for activity (4–9). The formation of the γ-secretase complex is tightly controlled, with an ordered assembly of subunits coupled to spatial restriction (10). It is believed that the last step of the complicated γ-secretase maturation and activation process involves in cis endoproteolysis of the PS holoprotein (11–13). It is this form of γ-secretase with PS in its N- and C-terminal fragments (NTF and CTF, respectively) that represents the fully mature, proteolytically active enzyme.γ-Secretase is a unique protease that cleaves within the lipid bilayer a large number of Type 1 single transmembrane-spanning proteins that vary widely in their sequence and size (14–16). In a previous report, we demonstrated that NCT functions as a substrate receptor for γ-secretase (4). In that report, we showed that NCT recruits substrates that have had their large extracellular domains first removed by an upstream protease in a process termed “ectodomain shedding.” This process generates a new, short extracellular stub with a free N terminus, which is required for proteolysis by γ-secretase. We also established that Glu-333 of NCT participates in activity within the larger context of the DYIGS and peptidase-like (DAP) domain, which shares distant homology to amino- and carboxypeptidases. A recent study by Chávez-Gutiérrez et al. (17) confirmed that mutations at the equivalent rodent residue impair γ-secretase. However, the authors attributed the reduction in activity to a role for Glu-333 in γ-secretase maturation but not directly in activity per se. Although a role for NCT and Glu-333 in γ-secretase assembly and maturation is consistent with our early work (4, 18, 19), the authors'' conclusion that mature γ-secretase complexes containing the Glu-333 mutant NCT are fully active presents a challenge to the model that NCT is a receptor for γ-secretase substrates in mature, active enzyme. Although PS-NTF or -CTF alone is an adequate measure of active γ-secretase complexes, Chávez-Gutiérrez et al. (17) measured specific activity by normalizing γ-secretase products to the sum of PS1-CTF and PEN-2 presumably due to the levels of PS-NTF/CTF by themselves being at the detection limit of Western blotting with electrochemiluminescence (ECL). Such an approach has caveats, as normalizing to the sum of PS1 and PEN-2 does not represent a measurement of the intrinsic activity per single, active enzyme; rather, this mode of normalization instead skews the data to minimize the effects of the mutations, especially when compounded with the unreliability of ECL measurement at the detection limit of Western blotting. Indeed, normalizing to the amount of mature, active γ-secretase in a rigorous, quantitative manner would be necessary to accurately compare the intrinsic activities of wild-type and mutant enzymes.In this study we used two γ-secretase reconstitution methods, including one that bypasses endoproteolysis and two separate normalization approaches to demonstrate that γ-secretase complexes containing NCT-E333A are indeed intrinsically less active than wild-type NCT. We show that this mutant is deficient in its ability to directly bind to γ-secretase substrates. Moreover, we confirm our observations with a second γ-secretase substrate, C83, which is itself the physiological product of α-secretase cleavage of APP. We also examine a series of substrate truncation mutants and find that γ-secretase can cleave substrates that lack the entire extracellular domain, provided that such substrates also contain a free N-terminal amine. Taken together, we conclude that Glu-333 participates directly in activity after γ-secretase complex maturation. Finally, we put forth a model wherein the dual role of Glu-333 in γ-secretase maturation and substrate recognition could be explained in the context of NCT being a substrate receptor. In this model Glu-333 partakes in the recruitment of not only the ectodomain-shed Type 1 membrane proteins but also of the intracellular loop of PS for its endoproteolysis, a hallmark event of γ-secretase maturation and activation.     

Widespread habitat for Europe's largest herbivores,but poor connectivity limits recolonization

Aim

Several large-mammal species in Europe have recovered and recolonized parts of their historical ranges. Knowing where suitable habitat exists, and thus where range expansions are possible, is important for proactively promoting coexistence between people and large mammals in shared landscapes. We aimed to assess the opportunities and limitations for range expansions of Europe's two largest herbivores, the European bison (Bison bonasus) and moose (Alces alces).

Location

Central Europe.

Methods

We used large occurrence datasets from multiple populations and species distribution models to map environmentally suitable habitats for European bison and moose across Central Europe, and to assess human pressure inside the potential habitat. We then used circuit theory modeling to identify potential recolonization corridors.

Results

We found widespread suitable habitats for both European bison (>120,000 km²) and moose (>244,000 km²), suggesting substantial potential for range expansions. However, much habitat was associated with high human pressure (37% and 43% for European bison and moose, respectively), particularly in the west of Central Europe. We identified a strong east–west gradient of decreasing connectivity, with major barriers likely limiting natural recolonization in many areas.

Main conclusions

We identify major potential for restoring large herbivores and their functional roles in Europe's landscapes. However, we also highlight considerable challenges for conservation planning and wildlife management, including areas where recolonization likely leads to human–wildlife conflict and where barriers to movement prevent natural range expansion. Conservation measures restoring broad-scale connectivity are needed in order to allow European bison and moose to recolonize their historical ranges. Finally, our analyses and maps indicate suitable but isolated habitat patches that are unlikely to be colonized but are candidate locations for reintroductions to establish reservoir populations. More generally, our work emphasizes that transboundary cooperation is needed for restoring large herbivores and their ecological roles, and to foster coexistence with people in Europe's landscapes.     

What factors shape female phenotypes of a poleward‐moving damselfly at the edge of its range?

Individuals at the expansion front during a climate‐driven range expansion are expected to differ phenotypically from those individuals in core populations. Little information is known about the joint, potentially opposing, effects of stressful conditions at the range edge versus evolutionary changes that take place during range expansion in shaping the phenotypes at the range front. We investigated the effect of range expansion on immune function, body condition and flight‐related morphology (flight muscle ratio, wing loading, and wing aspect ratio) of field‐collected females of the poleward‐moving damselfly Coenagrion scitulum. Individuals at the expansion front had a lower body condition, which indicated more stressful conditions at the range edge. Despite the counteracting effect of the shorter growth season, the higher flight muscle ratios at the expansion front indicated a strong selection for dispersal ability during range expansion. The current study suggests that models need to incorporate the interplay of stressful conditions and evolutionary processes at the expansion front to arrive at robust predictions of future species distributions under global warming. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 556–568.     

Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization

Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV). Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT). Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search), together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics. The model introduced can be generalized in order to analyze different biomineralizing organisms and to test different chemical pathways only by switching the system of mass transport equations.     

Differential Hepatic Metal and Metallothionein Levels in Three Feral Fish Species along a Metal Pollution Gradient

The accumulation of cadmium, copper and zinc and the induction of metallothioneins (MT) in liver of three freshwater fish species was studied. Gudgeon (Gobio gobio), roach (Rutilus rutilus) and perch (Perca fluviatilis) were captured at 6 sampling sites along a cadmium and zinc gradient and one reference site in a tributary of the Scheldt River in Flanders (Belgium).At each site up to 10 individuals per species were collected and analyzed on their general condition factor (K), hepatosomatic index (HSI) and gonadosomatic index (GSI). From each individual fish the liver was dissected and analyzed on Cd, Cu and Zn and MT-content. Although not all species were present at each site, hepatic Cd and Zn levels generally followed the pollution gradient and highest levels were measured in perch, followed by roach and gudgeon. Nevertheless also an effect of site was observed on this order. MT-levels appeared to be the highest in gudgeon although differences with the other species were not very pronounced and depended on the site. Significant relationships were found between hepatic zinc accumulation and MT levels. For each species the ratio MT_theoretical/ MT_measured was calculated, which gives an indication of the relative capacity to induce MTs and thus immobilize the metals. Perch had the lowest capacity in inducing MTs (highest ratio). Relationships between hepatic metal levels and fish condition indices were absent or very weak.     

Contrasting covariation of above- and belowground invertebrate species across plant genotypes

1. Invertebrate species generally do not respond independently to genotypic variation in plants, giving rise to clusters of species that naturally associate with or avoid certain genotypes. This covariation causes coevolution to be diffuse rather than pairwise. Studies on this topic, however, have never considered the belowground invertebrate community, leaving a critical gap in our understanding. 2. We investigated the covariation among naturally colonising above- and belowground invertebrate species across six genetically distinct populations of the dune grass Ammophila arenaria. After having grown from seed in a common garden, plants were randomised in a single field site to exclude all but broad-sense genetic variation. 3. Strong positive covariation across genotypes among both above- and belowground invertebrates was detected, while correlations between these two groups were negative. This clustering of above- and belowground species matched well with order level taxonomy. Host range, trophic level and food type on the other hand did not correspond well with the clusters. Within the cluster of aboveground fauna, subsequent groupings were not related to any phylogenetic or ecological characteristic, although correlations within these subgroups were very high. We furthermore demonstrated significant differences in multiple invertebrate species occurrence between plant genotypes, in general as well as at the above- and belowground level. 4. The observed strong covariation suggests diffuse coevolution between A. arenaria and its associated invertebrate species. The trade-off between root and shoot invertebrates could however hamper directional selection on resistance to either group. 5. Our results clearly demonstrate the need for studies of plant-animal interactions to include the belowground fauna, as this might drastically alter our general conception of how plants and their associated animal communities interact and how these interactions shape the process of evolution.     

Nematodes surfing the waves: long‐distance dispersal of soil‐borne microfauna via sea swept rhizomes

Dispersal mechanisms of soil‐borne microfauna have hitherto received little attention. Understanding dispersal mechanisms of these species is important to unravel their basic life history traits, biogeography, exchange of individuals between populations, and local adaptation. Soil‐borne nematodes and root‐feeding nematodes in particular occupy a key position in soil‐food webs and can be determinants for plant growth and vegetation structure and succession. However, their dispersal abilities have been scarcely addressed, predominantly focusing on species of agricultural importance. Still, root‐feeding nematodes are usually considered as being extremely limited and bound to the rhizosphere of plants. We investigated a mechanism for long distance dispersal of root‐feeding nematodes associated to two widespread coastal dune grasses. The nematodes are known to be crucial for the functioning of these grasses. We experimentally tested the hypothesis that root‐feeding nematodes are able to move across long distances inside rhizome fragments that are dispersed by seawater. We also tested the survival capacities of the host plants in seawater. Our study demonstrates that root‐feeding nematodes and plants are able to survive immersion in seawater, providing a mechanism for long distance dispersal of root feeding nematodes together with their host plant. Drifting rhizome fragments enable the exchange of plant material and animals between dune systems. These results provide new insights to understand the ecology of dune vegetation, the interaction with soil‐borne organisms and more importantly, re‐set the scale of spatial dynamics of a group of organisms considered extremely constrained in its dispersal capacities.