Workload characterization in a high-energy data grid and impact on resource management

The analysis of data usage in a large set of real traces from a high-energy physics collaboration revealed the existence of an emergent grouping of files that we coined “filecules”. This paper presents the benefits of using this file grouping for prestaging data and compares it with previously proposed file grouping techniques along a range of performance metrics. Our experiments with real workloads demonstrate that filecule grouping is a reliable and useful abstraction for data management in science Grids; that preserving time locality for data prestaging is highly recommended; that job reordering with respect to data availability has significant impact on throughput; and finally, that a relatively short history of traces is a good predictor for filecule grouping. Our experimental results provide lessons for workload modeling and suggest design guidelines for data management in data-intensive resource-sharing environments.

Turing Pattern Formation with Two Kinds of Cells and a Diffusive Chemical

We study a three-variable Turing system with two kinds of cells and a diffusive chemical, considering the formation and maintenance of fish skin patterns with multiple pigment cells. The two types of cells are produced from undifferentiated cells. They inhibit the supply rate of the other cell type, forming local clusters of the same cell type. In addition, the cells of one type can be maintained only in the presence of a diffusive chemical produced by the other cell type, resulting in the coexistence of two cell types in heterogeneous spatial patterns. We assume linear interaction among cells and the chemical, and cell supply rates constrained to be positive or zero. We derive the condition for diffusion-driven instability. In one-dimensional model, we examine how the wavelength of the periodic pattern depends on parameters. In the two-dimensional model, we study the condition for spot, stripe or reversed spot pattern to emerge (pattern selection). We discuss heuristic criteria for the pattern selection.     

Calcineurin ensures a link between the DNA replication checkpoint and microtubule-dependent polarized growth

Microtubules are central to eukaryotic cell morphogenesis. Microtubule plus-end tracking proteins (+TIPs) transport polarity factors to the cell cortex, thereby playing a key role in both microtubule dynamics and cell polarity. However, the signalling pathway linking +TIPs to cell polarity control remains elusive. Here we show that the fission yeast checkpoint kinase Cds1 (Chk2 homologue) delays the transition of growth polarity from monopolar to bipolar (termed NETO; new-end take-off). The +TIPs CLIP170 homologue Tip1 and kinesin Tea2 are responsible for this delay, which is accompanied by a reduction in microtubule dynamics at the cell tip. Remarkably, microtubule stabilization occurs asymmetrically, prominently at the non-growing cell end, which induces abnormal accumulation of the polarity factor Tea1. Importantly, NETO delay requires activation of calcineurin, which is carried out by Cds1, resulting in Tip1 dephosphorylation. Thus, our study establishes a critical link between calcineurin and checkpoint-dependent cell morphogenesis.     

Serological identification and molecular characterization of B (A) 02 subtype in patients and blood donors from Eastern China

This study was designed to identify the rare?type?ABO?blood?groups, B(A) 02, from Eastern China. Three samples with discordant serological results during routine blood type identification and four samples from one sample’ family were selected. All of them were detected by serological method. The exon 6 and 7 of the ABO genes were amplified by PCR and sequenced. They were typed as AsubB by serology and as BO by genotype. In AsubB samples, nt 700C>G mutation was detected in B gene, which was previously defined as B(A)02 alleles. In these seven samples, six showed B(A)02/O01 and one showed B(A)02/O02.B(A)02 allele was found to be more common in this study than B(A)04 which is considered to be more frequent than B(A)02. The careful identification of rare blood types is important for the safety of clinical blood transfusion.     

Zinc and iron concentration QTL mapped in a Triticum spelta × T. aestivum cross

Key message

Ten QTL underlying the accumulation of Zn and Fe in the grain were mapped in a set of RILs bred from the cross Triticum spelta × T. aestivum . Five of these loci (two for Zn and three for Fe) were consistently detected across seven environments.

Abstract

The genetic basis of accumulation in the grain of Zn and Fe was investigated via QTL mapping in a recombinant inbred line (RIL) population bred from a cross between Triticum spelta and T. aestivum. The concentration of the two elements was measured from grain produced in three locations over two consecutive cropping seasons and from a greenhouse trial. The range in Zn and Fe concentration across the RILs was, respectively, 18.8–73.5 and 25.3–59.5 ppm, and the concentrations of the two elements were positively correlated with one another (rp =+0.79). Ten QTL (five each for Zn and Fe accumulation) were detected, mapping to seven different chromosomes. The chromosome 2B and 6A grain Zn QTL were consistently expressed across environments. The proportion of the phenotype explained (PVE) by QZn.bhu-2B was >16 %, and the locus was closely linked to the SNP marker 1101425|F|0, while QZn.bhu-6A (7.0 % PVE) was closely linked to DArT marker 3026160|F|0. Of the five Fe QTL detected, three, all mapping to chromosome 1A were detected in all seven environments. The PVE for QFe.bhu-3B was 26.0 %.     

Environmental Fluctuations and Level of Density-Compensation Strongly Affects the Probability of Fixation and Fixation Times

The probability of, and time to, fixation of a mutation in a population has traditionally been studied by the classic Wright–Fisher model where population size is constant. Recent theoretical expansions have covered fluctuating populations in various ways but have not incorporated models of how the environment fluctuates in combination with different levels of density-compensation affecting fecundity. We tested the hypothesis that the probability of, and time to, fixation of neutral, advantageous and deleterious mutations is dependent on how the environment fluctuates over time, and on the level of density-compensation. We found that fixation probabilities and times were dependent on the pattern of autocorrelation of carrying capacity over time and interacted with density-compensation. The pattern found was most pronounced at small population sizes. The patterns differed greatly depending on whether the mutation was neutral, advantageous, or disadvantageous. The results indicate that the degree of mismatch between carrying capacity and population size is a key factor, rather than population size per se, and that effective population sizes can be very low also when the census population size is far above the carrying capacity. This study highlights the need for explicit population dynamic models and models for environmental fluctuations for the understanding of the dynamics of genes in populations.     

Genetic and clinical mosaicism in a patient with neurofibromatosis type 1

Patients with typical features of neurofibromatosis type 1 (NF1) limited to a specific body segment are usually referred to as having segmental NF1, which is generally assumed to be the result of somatic mosaicism for a NF1 mutation. Mosaicism has also been demonstrated at the molecular level in some sporadic cases with phenotypically classic NF1. In the present report, we describe a patient with NF1 disease manifestations throughout the whole body, but leaving a few sharply delineated segments of the skin unaffected, suggestive of revertant mosaicism. A large intragenic deletion was found by mutation analysis using long-range RT-PCR. The intra-exonic breakpoints were characterized in exon 13 and exon 28, resulting in a deletion of 99,571 bp at the genomic level. The presence of two genetically distinct cell populations, confirming mosaicism for this NF1 mutation, was shown by analysis of several tissues. Revertant mosaicism was excluded by demonstrating heterozygosity for markers residing in the deletion region. The findings in this patient demonstrate two things: (1) although the entire body is affected, mosaicism can still be suspected at clinical examination and proven by DNA analysis and skin biopsies; (2) long-range RT-PCR is a feasible method for demonstrating large intragenic deletions in NF1.     

Adaptive Dynamics of Altruistic Cooperation in a Metapopulation: Evolutionary Emergence of Cooperators and Defectors or Evolutionary Suicide?

We investigate the evolution of public goods cooperation in a metapopulation model with small local populations, where altruistic cooperation can evolve due to assortment and kin selection, and the evolutionary emergence of cooperators and defectors via evolutionary branching is possible. Although evolutionary branching of cooperation has recently been demonstrated in the continuous snowdrift game and in another model of public goods cooperation, the required conditions on the cost and benefit functions are rather restrictive, e.g., altruistic cooperation cannot evolve in a defector population. We also observe selection for too low cooperation, such that the whole metapopulation goes extinct and evolutionary suicide occurs. We observed intuitive effects of various parameters on the numerical value of the monomorphic singular strategy. Their effect on the final coexisting cooperator–defector pair is more complex: changes expected to increase cooperation decrease the strategy value of the cooperator. However, at the same time the population size of the cooperator increases enough such that the average strategy does increase. We also extend the theory of structured metapopulation models by presenting a method to calculate the fitness gradient in a general class of metapopulation models, and try to make a connection with the kin selection approach.     

Edraianthus × lakusicii (Campanulaceae) a new intersectional natural hybrid: morphological and molecular evidence

The genus Edraianthus A.DC. has a center of distribution in the Balkans and it is one of the most prominent groups of endemic plants in this region. During our recent fieldtrip to Mt. Lov?en (Montenegro), putative hybrid individuals were encountered, morphologically intermediate between two sympatric taxa, E. tenuifolius (E. sect. Edraianthus) and E. wettsteinii subsp. lovcenicus (E. sect. Uniflori). Multivariate morphometric and molecular analyses were carried out to investigate the occurrence of hybridization between these two species. As a result, a new nothospecies is described here, Edraianthus × lakusicii V. Stevanovi? & D. Laku?i?, a natural hybrid between E. tenuifolius and E. wettsteinii subsp. lovcenicus. At present, this hybrid is known only from the single locality of Mt. Lov?en. Its population size is estimated to be <50 mature individuals and the estimated “area of occupancy” is smaller than 1 km².     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

Cloning and expression of Penicillium minioluteum dextranase in Saccharomyces cerevisiae and its exploitation as a reporter in the detection of mycotoxins

A dextranase gene from Penicillium minioluteum (strain IMI068219) has been cloned, sequenced and expressed in Saccharomyces cerevisiae via fusion of the DNA segment encoding the mature dextranase protein with α-factor signal sequence, and insertion into the GAL1–controlled expression vector pYES2/CT. Galactose-induced expression yielded extracellular dextranase activity of 0.63 units/ml and cell-associated dextranase activity of 0.48 units/ml, after 24 h incubation. The dextranase construct was introduced into a strain of S. cerevisiae expressing the human cytochrome P450 3A4 (CYP3A4) and the cognate reductase, which was then used to develop a microplate toxicity bioassay. Toxicity was signalled as inhibition of dextranase activity, assayed fluorimetrically. This novel bioassay was assessed using six economically significant mycotoxins.     

Cytochrome c and superoxide

Wegerich et al. (J. Biol. Inorg. Chem. 18:429–440, 2013), working with singly modified human cytochromes c, claim to have found a new mechanism for the reduction of iron(III) cytochrome c by superoxide. I show that electron transfer by way of the solvent-accessible haem edge—a mechanism not considered by Wegerich et al.—is still the correct mechanism. Furthermore, several deficiencies in this work preclude any comparisons with other publications on this topic.     

Control and possible applications of a novel carrot-spoilage basidiomycete, Fibulorhizoctonia psychrophila

A novel cold-tolerant fungus, Fibulorhizoctonia psychrophila, was isolated from a refrigerated carrot storage facility and identified as an anamorph of Athelia, often classified in Rhizoctonia s.l. Growth of this fungus was observed between 0 and 20°C with an optimum at 9–12°C, while incubation of mycelium grown at 15–32°C resulted in absence of growth even after the fungus was transferred back to 15°C. Growth was inhibited in the presence of the antifungals sorbic acid or natamycin, in particular when the fungus was incubated at 18°C. F. psychrophila produces polysaccharide degrading enzymes that, when compared to enzymes from the ascomycete fungus Aspergillus niger, retain a larger proportion of their activity at lower temperatures. This indicates that F. psychrophila could be used as a source for novel industrial enzymes that are active at 4–15°C.     

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Key message

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement.

Abstract

Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.     

Thidiazuron-induced morphogenetic response in petiole cultures of Pelargonium × hortorum and Pelargonium × domesticum and its histological analysis

The possibility of inducing somatic embryogenesis in petiole cultures of two cultivars of Pelargonium × hortorum and of one cultivar of Pelargonium × domesticum using thidiazuron (TDZ) was investigated. Petioles were cultivated on a modified Murashige and Skoog medium with different concentrations and application periods of TDZ. Regeneration was achieved with all TDZ treatments for all cultivars and was highly variable. Shoots of different shapes and somatic embryo-like structures were observed. Histological examination revealed that no somatic embryos were formed, and regenerants had to be classified as shoots and shoot-like or leaf-like structures. The importance of these results on the classification of regeneration induced by TDZ in these species and on the propagation of these pelargoniums is discussed.     

Stochastic Models and Numerical Algorithms for a Class of Regulatory Gene Networks

Regulatory gene networks contain generic modules, like those involving feedback loops, which are essential for the regulation of many biological functions (Guido et al. in Nature 439:856–860, 2006). We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady-state distribution of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loops.     

Biological patterns and ecological indicators for Mediterranean fish and crustaceans below 1,000 m: a review

The Mediterranean Sea is a relatively deep, closed sea with high rates of fisheries exploitation. In recent years fishing activity has tended to shift towards deeper depths. At the same time, the Mediterranean displays some rather special hydrographic and biogeographic conditions. The present paper reviews the present state of knowledge of the fisheries, biology, and ecology of the deep-sea fish and crustacean species in the Mediterranean dwelling below 1,000 m with potential economic interest, placing special emphasis on the western basin, for which more data are available, as a basis for future studies of the ecology, biodiversity, and effects of climate change and exploitation in this zone. This review reveals that mediterranean deep-sea fishes and crustaceans employ highly conservative ecological strategies, and hence the low fecundity and low metabolic rates in a stable environment like the deep-sea make these populations highly vulnerable. Moreover, ripe females of the main species mentioned here concentrate in the deepest portions of their distribution ranges. Deep-sea fish and crustaceans have high trophic levels and low to medium omnivory index values. The ecological indices discussed here, in combination with the limited knowledge of deep-sea ecosystems, clearly call for an approach based on the Precautionary Principle.