Characterization and Reconstitution of Human Lipoyl Synthase (LIAS) Supports ISCA2 and ISCU as Primary Cluster Donors and an Ordered Mechanism of Cluster Assembly

Lipoyl synthase (LIAS) is an iron–sulfur cluster protein and a member of the radical S-adenosylmethionine (SAM) superfamily that catalyzes the final step of lipoic acid biosynthesis. The enzyme contains two [4Fe–4S] centers (reducing and auxiliary clusters) that promote radical formation and sulfur transfer, respectively. Most information concerning LIAS and its mechanism has been determined from prokaryotic enzymes. Herein, we detail the expression, isolation, and characterization of human LIAS, its reactivity, and evaluation of natural iron–sulfur (Fe–S) cluster reconstitution mechanisms. Cluster donation by a number of possible cluster donor proteins and heterodimeric complexes has been evaluated. [2Fe–2S]-cluster-bound forms of human ISCU and ISCA2 were found capable of reconstituting human LIAS, such that complete product turnover was enabled for LIAS, as monitored via a liquid chromatography–mass spectrometry (LC–MS) assay. Electron paramagnetic resonance (EPR) studies of native LIAS and substituted derivatives that lacked the ability to bind one or the other of LIAS’s two [4Fe–4S] clusters revealed a likely order of cluster addition, with the auxiliary cluster preceding the reducing [4Fe–4S] center. These results detail the trafficking of Fe–S clusters in human cells and highlight differences with respect to bacterial LIAS analogs. Likely in vivo Fe–S cluster donors to LIAS are identified, with possible connections to human disease states, and a mechanistic ordering of [4Fe–4S] cluster reconstitution is evident.     

Out-of-Field Hippocampus from Partial-Body Irradiated Mice Displays Changes in Multi-Omics Profile and Defects in Neurogenesis

The brain undergoes ionizing radiation exposure in many clinical situations, particularly during radiotherapy for brain tumors. The critical role of the hippocampus in the pathogenesis of radiation-induced neurocognitive dysfunction is well recognized. The goal of this study is to test the potential contribution of non-targeted effects in the detrimental response of the hippocampus to irradiation and to elucidate the mechanisms involved. C57Bl/6 mice were whole body (WBI) or partial body (PBI) irradiated with 0.1 or 2.0 Gy of X-rays or sham irradiated. PBI consisted of the exposure of the lower third of the mouse body, whilst the upper two thirds were shielded. Hippocampi were collected 15 days or 6 months post-irradiation and a multi-omics approach was adopted to assess the molecular changes in non-coding RNAs, proteins and metabolic levels, as well as histological changes in the rate of hippocampal neurogenesis. Notably, at 2.0 Gy the pattern of early molecular and histopathological changes induced in the hippocampus at 15 days following PBI were similar in quality and quantity to the effects induced by WBI, thus providing a proof of principle of the existence of out-of-target radiation response in the hippocampus of conventional mice. We detected major alterations in DAG/IP3 and TGF-β signaling pathways as well as in the expression of proteins involved in the regulation of long-term neuronal synaptic plasticity and synapse organization, coupled with defects in neural stem cells self-renewal in the hippocampal dentate gyrus. However, compared to the persistence of the WBI effects, most of the PBI effects were only transient and tended to decrease at 6 months post-irradiation, indicating important mechanistic difference. On the contrary, at low dose we identified a progressive accumulation of molecular defects that tended to manifest at later post-irradiation times. These data, indicating that both targeted and non-targeted radiation effects might contribute to the pathogenesis of hippocampal radiation-damage, have general implications for human health.     

Regulatory Light Chains in Cardiac Development and Disease

The role of regulatory light chains (RLCs) in cardiac muscle function has been elucidated progressively over the past decade. The RLCs are among the earliest expressed markers during cardiogenesis and persist through adulthood. Failing hearts have shown reduced RLC phosphorylation levels and that restoring baseline levels of RLC phosphorylation is necessary for generating optimal force of muscle contraction. The signalling mechanisms triggering changes in RLC phosphorylation levels during disease progression remain elusive. Uncovering this information may provide insights for better management of heart failure patients. Given the cardiac chamber-specific expression of RLC isoforms, ventricular RLCs have facilitated the identification of mature ventricular cardiomyocytes, opening up possibilities of regenerative medicine. This review consolidates the standing of RLCs in cardiac development and disease and highlights knowledge gaps and potential therapeutic advancements in targeting RLCs.     

Thermal analysis of polymer–water interactions and their relation to gas hydrate inhibition

Gas hydrates formed in oil production pipelines are crystalline solids where hydrocarbon gas molecules such as methane, propane, and their mixtures are trapped in a cagelike structure by hydrogen‐bonded water molecules to form undesirable plugs. Methanol and glycol are currently used to prevent these plugs via thermodynamic inhibition. Small amounts of water‐soluble polymers may provide an alternate approach for preventing gas hydrates. In this study, we expand the fundamental understanding of water–polymer systems with differential scanning calorimetry. Nonfreezable bound water was used to quantify polymer–water interactions and relate them to the chemical structure for a series of polymers, including acrylamides, cyclic lactams, and n‐vinyl amides. For good interactions, the water structure needs to be stabilized through hydrophobic interactions. An increased hydrophobicity of the pendant group also appears to favor polymer performance as a gas hydrate inhibitor. Good inhibitors, such as poly(diethyl acrylamide) and poly(N‐vinyl caprolactam), also show higher heat capacities, which indicate higher hydrophobicity, than poor performers such as polyzwitterions, in which hydrophilicity dominated. The phase behavior and thermodynamic properties of dilute polymer solutions were also evaluated through measurements of the heat of demixing and lower critical solution temperature. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 2642–2653, 2007     

SeaDoc: a self-adaptive document link provision system for framework extension tasks

It has been demonstrated that object-oriented frameworks can bring all kinds of advantages to application developers. To gain the advantages, application developers have to follow the framework-based development process. One step of the process is to integrate new components for framework extension. This is defined as a framework extension task in this work. In this task, application developers have to (1) retrieve examples, (2) acquire necessary documents, which are defined as the documents containing example adaptation information, and (3) adapt examples. Currently, acquiring necessary documents requires a lot of time because it is achieved through manually searching the Internet. Although there are many approaches to correctly acquiring those documents, the focus is never on time reduction. To satisfy the new criterion, we find the following challenging issues: (1) the dynamics of the valid document version, and (2) the uncertainty of the relevant necessary documents. The first issue is that the valid document version varies according to the framework version under which the retrieved example is workable. The second one is that the relevant necessary documents cannot be decided until a specific necessary document is specified. To resolve those two issues, a Self-adaptive Document link provision system, named SeaDoc, is provided in this work. SeaDoc resolves the dynamics by dynamically constructing document links with the corresponding valid document version. SeaDoc also resolves the uncertainty by adaptively selecting highly relevant document links. The experimental results show that SeaDoc reduces the time by 73 and 83 % compared with other two approaches.     

A holistic approach to protein structure alignment

A method of protein structure comparison developed previouslyis extended to incorporate other aspects of protein structurein addition to the inter-atomic vectors on which it was originallybased. Each additional aspect, which included hydrogen bonding,solvent exposure, torsional angles and sequence, was introducedseparately and evaluated for its ability to improve alignmentquality. The components were then combined, suitably weighted,to produce a more holistic comparison method. The method wastested on a group of remotely related ß/ type proteinsthat share a common feature in their overall chain fold. Theresults indicated that while the original inter-atomic vectorcomponent was sufficient to give the correct alignment of mostpairs of topologically equivalent proteins, the inclusion ofhydrogen bonds, torsion angles and a measure of solvent exposureled to improvements in the more difficult comparisons. Considerationof amino acid properties, including hydrophobicity, had no beneficialeffect. The failure of the latter component was not unexpectedconsidering the almost total lack of sequence similarity amongthe proteins considered.     

Feature extraction of the first difference of EMG time series for EMG pattern recognition

This paper demonstrates the utility of a differencing technique to transform surface EMG signals measured during both static and dynamic contractions such that they become more stationary. The technique was evaluated by three stationarity tests consisting of the variation of two statistical properties, i.e., mean and standard deviation, and the reverse arrangements test. As a result of the proposed technique, the first difference of EMG time series became more stationary compared to the original measured signal. Based on this finding, the performance of time-domain features extracted from raw and transformed EMG was investigated via an EMG classification problem (i.e., eight dynamic motions and four EMG channels) on data from 18 subjects. The results show that the classification accuracies of all features extracted from the transformed signals were higher than features extracted from the original signals for six different classifiers including quadratic discriminant analysis. On average, the proposed differencing technique improved classification accuracies by 2–8%.     

Influence of catalyst support geometry and wall thickness on NO x trap desulfation: rich/lean wobbling strategies and hexagonal cell supports for high SO2 selectivity during desulfation

Topics in Catalysis - This Synthetic Gas Bench (SGB) study focuses on the effect of cell geometry and wall thickness on the gasoline NO x trap functionality. The data show that besides a NO x trap...     

Responses of the Aphids Phorodon humuli and Rhopalosiphum padi to Sex Pheromone Stereochemistry in the Field

Gynoparous female and male damson-hop aphids, Phorodon humuli (Schrank), were caught in the field by water traps that were releasing the sex pheromone of this species, (1RS,4aR,7S,7aS)-nepetalactol. No behavioral activity was elicited by (4aS,7S,7aR)-nepetalactone, the major sex pheromone component of other aphid species such as Megoura viciae Buckton, even though olfactory cells were found in the secondary rhinaria on the third antennal segment of P. humuli that responded strongly to this compound. Gynoparous female P. humuli in the field responded less strongly to (1R,4aS,7S,7aR)-nepetalactol, the sex pheromone of the bird cherry-oat aphid, Rhopalosiphum padi (L.), than they did to the (4aR,7S,7aS)-nepetalactols, but males responded only to the latter. The (4aR,7S,7aS)-nepetalactone showed no electrophysiological activity so was not used in field trials. Releasing either the (4aS,7S,7aR)-nepetalactone or the (1R,4aS,7S,7aR)-nepetalactol with the (4aR,7S,7aS)-nepetalactols did not inhibit the response of P. humuli gynoparous females and males to the latter. Males of R. padi responded as strongly to the (4aR,7S,7aS)-nepetalactols as they did to (1R,4aS,7S,7aR)-nepetalactol. Males of P. humuli and R. padi responded positively to an increased concentration of the (4aR,7S,7aS)-nepetalactols released from two vials compared with that from a single vial, as did P. humuli (in one of two experiments) and R. padi to the (1RS,4aR,7S,7aS)- and (1R,4aS,7S,7aR)-nepetalactols when released together.