Investigating the cores of fossil systems with Chandra

We investigate the cores of fossil galaxy groups and clusters (`fossil systems') using archival Chandra data for a sample of 17 fossil systems. We determined the cool-core fraction for fossils via three observable diagnostics, the central cooling time, cuspiness, and concentration parameter. We quantified the dynamical state of the fossils by the X-ray peak/brightest cluster galaxy (BCG), and the X-ray peak/emission weighted centre separations. We studied the X-ray emission coincident with the BCG to detect the presence of potential thermal coronae. A deprojection analysis was performed for z < 0.05 fossils to obtain cooling time and entropy profiles, and to resolve subtle temperature structures. We investigated the Lx-T relation for fossils from the 400d catalogue to see if the scaling relation deviates from that of other groups. Most fossils are identified as cool-core objects via at least two cool-core diagnostics. All fossils have their dominant elliptical galaxy within 50 kpc of the X-ray peak, and most also have the emission weighted centre within that distance. We do not see clear indications of a X-ray corona associated with the BCG unlike that has been observed for some other objects. Fossils do not have universal temperature profiles, with some low-temperature objects lacking features that are expected for ostensibly relaxed objects with a cool-core. The entropy profiles of the z < 0.05 fossil systems can be well-described by a power law model, albeit with indices smaller than 1. The 400d fossils Lx-T relation shows indications of an elevated normalisation with respect to other groups, which seems to persist even after factoring in selection effects.Comment: Accepted for publication in Astronomy and Astrophysic

Dealing with change and uncertainty within the regulatory frameworks for flood defense infrastructure in selected European countries

Whereas existing literature on the interactions between law, adaptive governance and resilience in the water sector often focuses on quality or supply issues, this paper addresses adaptation in national water laws in relation to increasing flood risks. In particular, this paper analyzes the extent to which legal rules governing flood defense infrastructure in a selection of European countries (Sweden, France, England and the Netherlands) allow for response and adaptation to change and uncertainty. While there is evidence that the legal rules on the development of new infrastructure require that changing conditions be considered, the adaptation of existing infrastructure is a more complicated matter. Liability rules fail to adequately address damages resulting from causes external to the action or inaction of owners and managers, in particular extreme events. A trend towards clearer, and in some cases, increased public powers to ensure the safety of flood defense infrastructure is observed. The paper concludes that legal rules should ensure not only that decisions to build flood defenses are based on holistic and future-oriented assessments, but also that this is reflected in the implementation and operation of these structures

The European Union approach to flood risk management and improving societal resilience: lessons from the implementation of the Floods Directive in six European countries

Diversity in flood risk management approaches is often considered to be a strength. However in some national settings, and especially for transboundary rivers, variability and the incompatibility of approaches can reduce the effectiveness of flood risk management. Placed in the context of increasing flood risks, as well as the potential for flooding to undermine the European Union's sustainable development goals, a desire to increase societal resilience to flooding has prompted the introduction of a common European Framework. This paper provides a legal and policy analysis of the implementation of the Floods Directive (2007/60/EC) in six countries; Belgium (Flemish Region), England, France, the Netherlands, Poland and Sweden. Evaluation criteria from existing legal and policy literature frame the study of the Directive and its impact on enhancing or constraining societal resilience by using an adaptive governance approach. These criteria are initially used to analyze the key components of the EU approach, before providing insight of the implementation of the Directive at a national level. Similarities and differences in the legal translation of European goals into existing flood risk management are analyzed alongside their relative influence on policy and practice. The research highlights that the impact of the Floods Directive on increasing societal resilience has been nationally variable, in part due to its focus on procedural obligations, rather than on more substantive requirements. Analysis shows that despite a focus on transboundary river basin management, in some cases existing traditions of flood risk management, have overridden objectives to harmonize flood risk management. This could be strengthened by requiring more stringent cooperation and providing the competent authorities in International River Basins Districts with more power. Despite some shortcomings in directly impacting flood risk outcomes, the Directive has positively stimulated discussion and flood risk management planning in countries that were perhaps lagging behind

Accessing the solid electrolyte interphase on silicon anodes for lithium ion batteries in situ through transmission soft X ray absorption spectroscopy

Silicon offers nine times higher theoretical storage capacity than commercial graphite anodes for Li ion batteries. For cycling stability, the electrolyte needs to be kinetically stabilized by the so called Solid Electrolyte Interphase SEI , a layer which ideally forms once from decomposition products of the electrolyte. While it works for graphite, the SEI on silicon fails to stabilize the electrolyte sufficiently, partly due to the large volume changes upon de lithiation. To investigate the SEI on silicon anodes, we developed a novel approach for X ray Absorption Spectroscopy XAS , that puts a twist to conventional SiNx window based liquid cells by utilizing a deliberately induced gas bubble to form a soft X ray transparent electrolyte layer. We demonstrate our approach to allow transmission XAS in the soft X ray regime on liquids and electrode thin film materials under in situ conditions. In our case XAS study of the SEI on silicon anodes, we reveal the main SEI constituents as Li acetate, Li ethylene di carbonate or Li ethylene mono carbonate, Li acetylacetonate, LiOH, and LiF. Additionally, we see evidence for aldehyde species which we attribute to possible liquid inclusions within a porous SEI morphology.We consider our method an appropriate tool for the successful engineering of a stable, efficient SEI in the futur

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

The metabolism of organisms can be studied with comprehensive stoichiometric models of their metabolic networks. Flux balance analysis (FBA) calculates optimal metabolic performance of stoichiometric models. However, detailed biological interpretation of FBA is limited because, in general, a huge number of flux patterns give rise to the same optimal performance. The complete description of the resulting optimal solution spaces was thus far a computationally intractable problem. Here we present CoPE-FBA: Comprehensive Polyhedra Enumeration Flux Balance Analysis, a computational method that solves this problem. CoPE-FBA indicates that the thousands to millions of optimal flux patterns result from a combinatorial explosion of flux patterns in just a few metabolic sub-networks. The entire optimal solution space can now be compactly described in terms of the topology of these sub-networks. CoPE-FBA simplifies the biological interpretation of stoichiometric models of metabolism, and provides a profound understanding of metabolic flexibility in optimal states

Evaluating pathway enumeration algorithms in metabolic engineering case studies

The design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Generation and the Find Path algorithms. Both are capable of enumerating exhaustively multiple pathways using network topology. We study their capabilities and limitations when designing novel heterologous pathways, by applying these methods on two case studies of synthetic metabolic engineering related to the production of butanol and vanillin

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads

Immunogenicity of a Promiscuous T Cell Epitope Peptide Based Conjugate Vaccine against Benzo[a]pyrene: Redirecting Antibodies to the Hapten

The prototype polycyclic aromatic hydrocarbon benzo[a]pyrene (B[a]P) is an environmental pollutant and food contaminant of epidemiological importance. To protect against adverse effects of this ubiquitous carcinogen, we developed an immunoprophylactic strategy based on a B[a]P-protein conjugate vaccine to induce B[a]P specific antibodies (Grova et al., Vaccine. 2009;27:4142–51). Here, we investigated in mice the efficacy of B[a]P-peptide conjugates based on promiscuous T cell epitopes (TCE) into further improve this approach. We showed that B[a]P-peptide conjugates induced very different levels of hapten-specific antibodies with variable functional efficacy, depending on the carrier. In some cases peptide carriers induced a more efficient antibody response against B[a]P than tetanus toxoid as a protein carrier, with the capacity to sequester more B[a]P in the blood. Reducing the carrier size to a single TCE can dramatically shift the antibody bias from the carrier to the B[a]P. Conjugates based on the TCE FIGITEL induced the best anti-hapten response and no antibodies against the carrier peptide. Some peptide conjugates increased the selectivity of the antibodies for the activated metabolite 7,8-diol-B[a]P and B[a]P by one or two orders of magnitude. The antibody efficacy was also demonstrated in their ability to sequester B[a]P in the blood and modulate its faecal excretion (15–56%). We further showed that pre-existing immunity to the carrier from which the TCE was derived did not reduce the immunogenicity of the peptide conjugate. In conclusion, we showed that a vaccination against B[a]P using promiscuous TCEs of tetanus toxin as carriers is feasible even in case of a pre-existing immunity to the toxoid and that some TCE epitopes dramatically redirect the antibody response to the hapten. Further studies to demonstrate a long-term protection of an immunoprophylactic immunisation against B[a]P are warranted