Multi-electron transitions induced by neutron impact on helium

We explore excitation and ionization by neutron impact as a novel tool for the investigation of electron-electron correlations in helium. We present single and double ionization spectra calculated in accurate numerical ab-initio simulations for incoming neutrons with kinetic energies of up to 150 keV. The resulting electron spectra are found to be fundamentally different from photoioniza- tion or charged particle impact due to the intrinsic many-body character of the interaction. In particular, doubly excited resonances that are strongly suppressed in electron or photon impact become prominent. The ratio of double to single ionization is found to differ significantly from those of photon and charged particle impact.Comment: 5 pages, 5 figure

Proteasome alpha-type subunit C9 is a primary target of autoantibodies in sera of patients with myositis and systemic lupus erythematosus

Autoantibodies occur in low frequencies among patients with myositis characterizing only distinct subsets of this disease. Most of these known antibodies are directed to enzymatically active complexes. The 20S proteasome represents an essential cytoplasmatic protein complex for intracellular nonlysosomal protein degradation, and is involved in major histocompatibility complex class I restricted antigen processing. In this study we investigated whether the 20S proteasome complex is an antibody target in myositis and in other autoimmune diseases. 34 sera of poly/dermatomyositis patients were assayed for antiproteasomal antibodies using enzyme-linked immunosorbent assay, immunoblot, and two-dimensional non-equilibrium pH gradient electrophoresis (NEPHGE). Sera was from patients with systemic lupus erythematosus (SLE), mixed connective tissue disease, and rheumatoid arthritis; healthy volunteers served as controls. In 62% (21/34) of the cases sera from patients with myositis and in 58% (30/52) of the cases sera from patients with SLE reacted with the 20S proteasome. These frequencies exceeded those of sera from patients with mixed connective tissue disease, rheumatoid arthritis, and healthy controls. The alpha-type subunit C9 of the 20S proteasome was determined to be the predominant target of the autoimmune sera in myositis and SLE. Lacking other frequent autoantibodies in myositis, the antiproteasome antibodies are the most common humoral immune response so far detected in this disease entity

Light-Induced Metastable Magnetic Texture Uncovered by in situ Lorentz Microscopy

Magnetic topological defects, such as vortices and Skyrmions, can be stabilized as equilibrium structures in nanoscale geometries and by tailored intrinsic magnetic interactions. Here, employing rapid quench conditions, we report the observation of a light-induced metastable magnetic texture, which consists of a dense nanoscale network of vortices and antivortices. Our results demonstrate the emergence of ordering mechanisms in quenched optically driven systems, which may give a general access to novel magnetic structures on nanometer length scales

Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis

Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment

Fano Resonances in Electronic Transport through a Single Electron Transistor

We have observed asymmetric Fano resonances in the conductance of a single electron transistor resulting from interference between a resonant and a nonresonant path through the system. The resonant component shows all the features typical of quantum dots, but the origin of the non-resonant path is unclear. A unique feature of this experimental system, compared to others that show Fano line shapes, is that changing the voltages on various gates allows one to alter the interference between the two paths.Comment: 8 pages, 6 figures. Submitted to PR

The fate of the homoctenids (Tentaculitoidea) during the Frasnian-Famennian mass extinction (Late Devonian)

The homoctenids (Tentaculitoidea) are small, conical-shelled marine animals which are amongst the most abundant and widespread of all Late Devonian fossils. They were a principal casualty of the Frasnian-Famennian (F-F, Late Devonian) mass extinction, and thus provide an insight into the extinction dynamics. Despite their abundance during the Late Devonian, they have been largely neglected by extinction studies. A number of Frasnian-Famennian boundary sections have been studied, in Poland, Germany, France, and the United States. These sections have yielded homoctenids, which allow precise recognition of the timing of the mass extinction. It is clear that the homoctenids almost disappear from the fossil record during the latest Frasnian “Upper Kellwasser Event”. The coincident extinction of this pelagic group, and the widespread development of intense marine anoxia within the water column, provides a causal link between anoxia and the F-F extinction. Most notable is the sudden demise of a group, which had been present in rock-forming densities, during this anoxic event. One new species, belonging to Homoctenus is described, but is not formally named here

Development of a framework for metabolic pathway analysis-driven strain optimization methods

Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands. Additionally, their complex parameterization and lack of intuitive tools pose an important challenge towards making these widely available to the community. Recently, MCSEnumerator has extended the scale of these methods, namely regarding enumeration of minimal cut sets, now able to handle GSMMs. This work proposes a tool implementing this method as a Java library and a plugin within the OptFlux metabolic engineering platform providing a friendly user interface. A standard enumeration problem and pipeline applicable to GSMMs is proposed, making use by the community simpler. To highlight the potential of these approaches, we devised a case study for overproduction of succinate, providing a phenotype analysis of a selected strategy and comparing robustness with a selected solution from a bi-level CSOM.The authors thank the project “DeYeastLibrary—Designer yeast strain library optimized for metabolic engineering applications”, Ref. ERA-IB-2/0003/2013, funded by national funds through “Fundação para a Ciência e Tecnologia / Ministério da Ciência, Tecnologia e Ensino Superior”.info:eu-repo/semantics/publishedVersio

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.

Inverse modelling of European CH4 emissions during 2006-2012 using different inverse models and reassessed atmospheric observations

We present inverse modelling (top down) estimates of European methane (CH4) emissions for 2006-2012 based on a new quality-controlled and harmonised in situ data set from 18 European atmospheric monitoring stations. We applied an ensemble of seven inverse models and performed four inversion experiments, investigating the impact of different sets of stations and the use of a priori information on emissions.The inverse models infer total CH4 emissions of 26.8 (20.2-29.7) TgCH(4) yr(-1) (mean, 10th and 90th percentiles from all inversions) for the EU-28 for 2006-2012 from the four inversion experiments. For comparison, total anthropogenic CH4 emissions reported to UNFCCC (bottom up, based on statistical data and emissions factors) amount to only 21.3 TgCH(4) yr(-1) (2006) to 18.8 TgCH(4) yr(-1) (2012). A potential explanation for the higher range of top-down estimates compared to bottom-up inventories could be the contribution from natural sources, such as peatlands, wetlands, and wet soils. Based on seven different wetland inventories from the Wetland and Wetland CH4 Inter-comparison of Models Project (WETCHIMP), total wetland emissions of 4.3 (2.3-8.2) TgCH(4) yr(-1) from the EU-28 are estimated. The hypothesis of significant natural emissions is supported by the finding that several inverse models yield significant seasonal cycles of derived CH4 emissions with maxima in summer, while anthropogenic CH4 emissions are assumed to have much lower seasonal variability. Taking into account the wetland emissions from the WETCHIMP ensemble, the top-down estimates are broadly consistent with the sum of anthropogenic and natural bottom-up inventories. However, the contribution of natural sources and their regional distribution remain rather uncertain.Furthermore, we investigate potential biases in the inverse models by comparison with regular aircraft profiles at four European sites and with vertical profiles obtained during the Infrastructure for Measurement of the European Carbon Cycle (IMECC) aircraft campaign. We present a novel approach to estimate the biases in the derived emissions, based on the comparison of simulated and measured enhancements of CH4 compared to the background, integrated over the entire boundary layer and over the lower troposphere. The estimated average regional biases range between -40 and 20% at the aircraft profile sites in France, Hungary and Poland.</p