Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2

Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels.

Combined static and dynamic assertion-based debugging of constraint logic programs

We propose a general framework for assertion-based debugging of constraint logic programs. Assertions are linguistic constructions for expressing properties of programs. We define several assertion schemas for writing (partial) specifications for constraint logic programs using quite general properties, including user-defined programs. The framework is aimed at detecting deviations of the program behavior (symptoms) with respect to the given assertions, either at compile-time (i.e., statically) or run-time (i.e., dynamically). We provide techniques for using information from global analysis both to detect at compile-time assertions which do not hold in at least one of the possible executions (i.e., static symptoms) and assertions which hold for all possible executions (i.e., statically proved assertions). We also provide program transformations which introduce tests in the program for checking at run-time those assertions whose status cannot be determined at compile-time. Both the static and the dynamic checking are provably safe in the sense that all errors flagged are definite violations of the pecifications. Finally, we report briefly on the currently implemented instances of the generic framework.

Effectiveness of combined sharing and freeness analysis using abstract interpretation

This paper presents improved unification algorithms, an implementation, and an analysis of the effectiveness of an abstract interpreter based on the sharing + freeness domain presented in a previous paper, which was designed to accurately and concisely represent combined freeness and sharing information for program variables. We first briefly review this domain and the unification algorithms previously proposed. We then improve these algorithms and correct them to deal with some cases which were not well analyzed previously, illustrating the improvement with an example. We then present the implementation of the improved algorithm and evaluate its performance by comparing the effectiveness of the information inferred to that of other interpreters available to us for an application (program parallelization) that is common to all these interpreters. All these systems have been embedded in a real parallelizing compiler. Effectiveness of the analysis is measured in terms of actual final performance of the system: i.e. in terms of the actual speedups obtained. The results show good performance for the combined domain in that it improves the accuracy of both types of information and also in that the analyzer using the combined domain is more effective in the application than any of the other analyzers it is compared to.

Safety and health in forest harvesting operations. Diagnosis and preventive actions. A review

Aim of study: to review the present state of the art in relation to the main labour risks and the most relevant results of recent studies evaluating the safety and health conditions of the forest harvesting work and better ways to reduce accidents. Area of study: It focuses mainly on developed Countries, where the general concern about work risks prevention, together with the complex idiosyncrasy of forest work in forest harvesting operations, has led to a growing interest from the forest scientific and technical community. Material and Methods: The main bibliographic and Internet references have been identified using common reference analysis tools. Their conclusions and recommendations have been comprehensively summarized. Main results: Collection of the principal references and their most important conclusions relating to the main accident risk factors, their causes and consequences, the means used towards their prevention, both instrumental as well as in the aspects of training and business management, besides the influence of the growing mechanization of logging operations on those risks. Research highlights: Accident risk is higher in forest harvesting than in most other work sectors, and the main risk factors such as experience, age, seasonality, training, protective equipment, mechanization degree, etc. have been identified and studied. The paper summarizes some relevant results, one of the principal being that the proper entrepreneurial risk management is a key factor leading to the success in minimizing labour risks..

The impact of the economic crisis and policy actions on GHG emissions from road transport in Spain

Road traffic is the greatest contributor to the carbon footprint of the transport sector and reducing it has become one of the main targets of sustainable transport policies. An analysis of the main factors influencing greenhouse gas (GHG) emissions is essential for designing new energy- and environmentally efficient strategies for the road transport. This paper addresses this need by (i) identifying factors which influence the carbon footprint, including traffic activity, fuel economy and socioeconomic development; and (ii) proposing a methodological framework which uses Modified Laspeyres Index decomposition to analyze the effect of important drivers on the changes in emissions of road transport in Spain during the period from 1990 to 2010. The results demonstrate that the country׳s economic growth has been closely linked to the rise in GHG emissions. The innovative contribution of this paper is the special analysis of the changes in mobility patterns and GHG emissions during the economic crisis, when, for the first time, Spanish road traffic emissions decreased. The reduction of road transport and improved energy efficiency has been powerful contributors to this decrease, demonstrating the effectiveness of energy-saving measures. On the basis of this analysis, several tailored policy recommendations have been suggested for future implementation.

Characteristics of the turbulent/nonturbulent interface in boundary layers, jets and shear-free turbulence

The characteristics of turbulent/nonturbulent interfaces (TNTI) from boundary layers, jets and shear-free turbulence are compared using direct numerical simulations. The TNTI location is detected by assessing the volume of turbulent flow as function of the vorticity magnitude and is shown to be equivalent to other procedures using a scalar field. Vorticity maps show that the boundary layer contains a larger range of scales at the interface than in jets and shear-free turbulence where the change in vorticity characteristics across the TNTI is much more dramatic. The intermittency parameter shows that the extent of the intermittency region for jets and boundary layers is similar and is much bigger than in shear-free turbulence, and can be used to compute the vorticity threshold defining the TNTI location. The statistics of the vorticity jump across the TNTI exhibit the imprint of a large range of scales, from the Kolmogorov micro-scale to scales much bigger than the Taylor scale. Finally, it is shown that contrary to the classical view, the low-vorticity spots inside the jet are statistically similar to isotropic turbulence, suggesting that engulfing pockets simply do not exist in jets

DNA bending and the initiation of transcription at σ54-dependent bacterial promoters

We have examined the effects on transcription initiation of promoter and enhancer strength and of the curvature of the DNA separating these entities on wild-type and mutated enhancer–promoter regions at the Escherichia coli σ54-dependent promoters glnAp2 and glnHp2 on supercoiled and linear DNA. Our results, together with previously reported observations by other investigators, show that the initiation of transcription on linear DNA requires a single intrinsic or induced bend in the DNA, as well as a promoter with high affinity for σ54-RNA polymerase, but on supercoiled DNA requires either such a bend or a high affinity promoter but not both. The examination of the DNA sequence of all nif gene activator- or nitrogen regulator I-σ54 promoters reveals that those lacking a binding site for the integration host factor have an intrinsic single bend in the DNA separating enhancer from promoter.

Functional analysis of DNA bending and unwinding by the high mobility group domain of LEF-1

LEF-1 (lymphoid enhancer-binding factor 1) is a cell type-specific member of the family of high mobility group (HMG) domain proteins that recognizes a specific nucleotide sequence in the T cell receptor (TCR) α enhancer. In this study, we extend the analysis of the DNA-binding properties of LEF-1 and examine their contributions to the regulation of gene expression. We find that LEF-1, like nonspecific HMG-domain proteins, can interact with irregular DNA structures such as four-way junctions, albeit with lower efficiency than with specific duplex DNA. We also show by a phasing analysis that the LEF-induced DNA bend is directed toward the major groove. In addition, we find that the interaction of LEF-1 with a specific binding site in circular DNA changes the linking number of DNA and unwinds the double helix. Finally, we identified two nucleotides in the LEF-1-binding site that are important for protein-induced DNA bending. Mutations of these nucleotides decrease both the extent of DNA bending and the transactivation of the TCRα enhancer by LEF-1, suggesting a contribution of protein-induced DNA bending to the function of TCRα enhancer.