Properties of the DREAM scheme and its optimization for application to proteins

The DREAM scheme is an efficient adiabatic homonuclear polarization-transfer method suitable for multi-dimensional experiments in biomolecular solid-state NMR. The bandwidth and dynamics of the polarization transfer in the DREAM experiment depend on a number of experimental and spin-system parameters. In order to obtain optimal results, the dependence of the cross-peak intensity on these parameters needs to be understood and carefully controlled. We introduce a simplified model to semi-quantitatively describe the polarization-transfer patterns for the relevant spin systems. Numerical simulations for all natural amino acids (except tryptophane) show the dependence of the cross-peak intensities as a function of the radio-frequency-carrier position. This dependency can be used as a guide to select the desired conditions in protein spectroscopy. Practical guidelines are given on how to set up a DREAM experiment for optimized Cα/Cβ transfer, which is important in sequential assignment experiment

Microbial iron reduction during passive in situ remediation of an acidic mine pit lake mesocosm

AbstractFerric iron reduction was studied in a pilot-scale enclosure experiment for passive biological remediation of an acidic mine pit lake in Lusatia, Germany. The metabolic properties of prokaryotes involved in Fe(III) reduction may be important for the outcome of biological remediation, as chemolithotrophic Fe(III) reduction can counteract the desired pH increase, but heterotrophic Fe(III) reduction will provide the necessary Fe(II) for precipitation of sulfide minerals following sulfate reduction. Therefore, vertical profiles of sediment parameters related to iron and sulfur cycling were determined in conjunction with viable counts of different ferric iron-reducing micro-organisms using selective media. Findings were compared to an untreated reference site. The addition of organic matter stimulated ferric iron reduction and sulfate reduction in the enclosure and led to elevated pH and accumulations of ferrous iron and reduced sulfur compounds. Numbers of neutrophilic heterotrophic Fe(III) reducers increased during treatment, those of acidophilic heterotrophic Fe(III) reducers remained similar, and those of acidophilic chemolithotrophic Fe(III) reducers decreased. Zones of ferric iron-reducing activity corresponded well with microbial depth profiles; however, viable counts of neutrophilic or acid-tolerant Fe(III) reducers must have been underestimated based on the corresponding observed activity levels. Ferric iron reduction by chemolithotrophic acidophiles seemed to be of minor importance, so a lowering of pH values due to Fe(III) reducing activity is unlikely

Measurement of compartment pressure of the rectus sheath during intra-abdominal hypertension in rats

Objective: To investigate whether the compartment pressure of the rectus sheath (CPRS) reflects the intra-abdominal pressure (IAP) under various conditions of intra-abdominal hypertension (IAH). Design and setting: Prospective experimental study with in vivo pressure measurements at the Institute for Clinical and Experimental Surgery, University of Saarland. Animals: Sprague-Dawley rats. Interventions: Stepwise increase and decrease in IAP with continuous measurement of the correspondent CPRS. Measurements and results: Physiological IAP (2 mmHg) and CPRS (6 mmHg) showed astatistically significant difference. Stepwise elevation in IAP was associated with asimultaneous increase in CPRS. Accordingly, stepwise decompression of IAP resulted in astepwise decrease in CPRS. Under both conditions Bland-Altman analysis comparing IAP to correspondent CPRS showed avery good agreement for IAP at or above 12 mmHg. In addition, closure of the overlaying subcutaneous tissue and skin did not affect CPRS or its correlation with IAP. Conclusions: CPRS accurately reflects IAP for IAP of 12 mmHg or higher. Thus CPRS measurements may represent anovel approach for diagnosis and monitoring of IA

Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides

<p>Abstract</p> <p>Background</p> <p>Plant natriuretic peptides (PNPs) are a class of systemically mobile molecules distantly related to expansins. While several physiological responses to PNPs have been reported, their biological role has remained elusive. Here we use a combination of expression correlation analysis, meta-analysis of gene expression profiles in response to specific stimuli and in selected mutants, and promoter content analysis to infer the biological role of the <it>Arabidopsis thaliana </it>PNP, AtPNP-A.</p> <p>Results</p> <p>A gene ontology analysis of <it>AtPNP-A </it>and the 25 most expression correlated genes revealed a significant over representation of genes annotated as part of the systemic acquired resistance (SAR) pathway. Transcription of these genes is strongly induced in response to salicylic acid (SA) and its functional synthetic analogue benzothiadiazole S-methylester (BTH), a number of biotic and abiotic stresses including many SA-mediated SAR-inducing conditions, as well as in the constitutive SAR expressing mutants <it>cpr5 </it>and <it>mpk4 </it>which have elevated SA levels. Furthermore, the expression of <it>AtPNP-A </it>was determined to be significantly correlated with the SAR annotated transcription factor, <it>WRKY 70</it>, and the promoters of <it>AtPNP-A </it>and the correlated genes contain an enrichment in the core WRKY binding W-box <it>cis</it>-elements. In constitutively expressing <it>WRKY 70 </it>lines the expression of <it>AtPNP-A </it>and the correlated genes, including the SAR marker genes, <it>PR-2 </it>and <it>PR-5</it>, were determined to be strongly induced.</p> <p>Conclusion</p> <p>The co-expression analyses, both in wild type and mutants, provides compelling evidence that suggests <it>AtPNP-A </it>may function as a component of plant defence responses and SAR in particular. The presented evidence also suggests that the expression of <it>AtPNP-A </it>is controlled by WRKY transcription factors and WRKY 70 in particular. <it>AtPNP-A </it>shares many characteristics with PR proteins in that its transcription is strongly induced in response to pathogen challenges, it contains an N-terminal signalling peptide and is secreted into the extracellular space and along with PR-1, PR-2 and PR-5 proteins it has been isolated from the Arabidopsis apoplast. Based on these findings we suggest that <it>AtPNP-A </it>could be classified as a newly identified PR protein.</p

Second harmonic generation from plasmonic hotspots by controlled local symmetry breaking

Bonding resonant modes of plasmonic nanoantennas with narrow gaps exhibit very large local field enhancement. These hotspots are highly attractive for boosting optical nonlinearities, such as second harmonic generation. However, for resonant symmetric gap antennas, the strong second harmonic sources created at the gap interfaces oscillate out-of-phase and therefore interfere destructively in the far-field. Here, we use an advanced nanofabrication approach to systematically break the local symmetry of nanoscopic antenna gaps while retaining the bonding resonant antenna mode at the fundamental frequency and the concomitant intensity hotspot. We find that antennas with the strongest local symmetry breaking emit correspondingly intense second harmonic radiation as compared to symmetric reference structures. By combining these findings with second harmonic radiation patterns as well as quantitative nonlinear simulations, we obtain remarkably detailed insights into the mechanism of second harmonic generation at the nanoscale. Our findings open new perspectives for the realization of non-reciprocal nanoscale systems, where local symmetry breaking is crucial to create unique functionalities

Characterization and Compensation of Network-Level Anomalies in Mixed-Signal Neuromorphic Modeling Platforms

Advancing the size and complexity of neural network models leads to an ever increasing demand for computational resources for their simulation. Neuromorphic devices offer a number of advantages over conventional computing architectures, such as high emulation speed or low power consumption, but this usually comes at the price of reduced configurability and precision. In this article, we investigate the consequences of several such factors that are common to neuromorphic devices, more specifically limited hardware resources, limited parameter configurability and parameter variations. Our final aim is to provide an array of methods for coping with such inevitable distortion mechanisms. As a platform for testing our proposed strategies, we use an executable system specification (ESS) of the BrainScaleS neuromorphic system, which has been designed as a universal emulation back-end for neuroscientific modeling. We address the most essential limitations of this device in detail and study their effects on three prototypical benchmark network models within a well-defined, systematic workflow. For each network model, we start by defining quantifiable functionality measures by which we then assess the effects of typical hardware-specific distortion mechanisms, both in idealized software simulations and on the ESS. For those effects that cause unacceptable deviations from the original network dynamics, we suggest generic compensation mechanisms and demonstrate their effectiveness. Both the suggested workflow and the investigated compensation mechanisms are largely back-end independent and do not require additional hardware configurability beyond the one required to emulate the benchmark networks in the first place. We hereby provide a generic methodological environment for configurable neuromorphic devices that are targeted at emulating large-scale, functional neural networks

A unique serpin P1′ glutamate and a conserved β-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin)

SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. KLK7 (kallikrein 7) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1′) of the vaspin reactive centre loop is fairly rigid compared with the flexible residues before P2, possibly supported by an ionic interaction of P1′ glutamate (Glu379) with an arginine residue (Arg302) of the β-sheet C. A P1′ glutamate seems highly unusual and unfavourable for the protease KLK7. We characterized vaspin mutants to investigate the roles of these two residues in protease inhibition and recognition by vaspin. Reactive centre loop mutations changing the P1′ residue or altering the reactive centre loop conformation significantly increased inhibition parameters, whereas removal of the positive charge within β-sheet C impeded the serpin–protease interaction. Arg302 is a crucial contact to enable vaspin recognition by KLK7 and it supports moderate inhibition of the serpin despite the presence of the detrimental P1′ Glu379, which clearly represents a major limiting factor for vaspin-inhibitory activity. We also show that the vaspin-inhibition rate for KLK7 can be modestly increased by heparin and demonstrate that vaspin is a heparin-binding serpin. Noteworthily, we observed vaspin as a remarkably thermostable serpin and found that Glu379 and Arg302 influence heat-induced polymerization. These structural and functional results reveal the mechanistic basis of how reactive centre loop sequence and exosite interaction in vaspin enable KLK7 recognition and regulate protease inhibition as well as stability of this adipose tissue-derived serpin

Direct electrical modulation of surface response in a single plasmonic nanoresonator

Classical electrodynamics describes the optical response of macroscopic systems, where the boundaries between materials is treated as infinitesimally thin. However, due to the quantum nature of electrons, interfaces acquires a finite thickness. To include non-classical surface effects in the framework of Maxwell's equations, surface-response functions can be introduced, also known as Feibelman $d$-parameters. Surface response impacts systems with strong field localization at interfaces, which is encountered in noble metal nanoparticles supporting surface plasmon polaritons. However, studying surface response is challenging as it necessitates sub-nanometer control of geometric features, e.g. the gap size in a dimer antenna, while minimizing uncertainties in morphology. In contrast, electrical gating is convenient since the static screening charges are confined exclusively to the surface, which alleviates the need for precise control over the morphology. Here, we study the perturbation of Feibelman $d$-parameters by direct electric charging of a single plasmonic nanoresonator and investigate the resulting changes of the resonance in experiment and theory. The measured change of the resonance frequency matches the theory by assuming a perturbation of the tangential surface current. However, we also observe an unforeseen narrowing in the resonance width when adding electrons to the surface of a plasmonic nanoresonator. These reduced losses cannot be explained by electron spill-out within the local-response approximation (LRA). Such an effect is likely caused by nonlocality and the anisotropy of the perturbed local permittivity. Our findings open up possibilities to reduce losses in plasmonic resonators and to develop ultrafast and extremely small electrically driven plasmonic modulators and metasurfaces by leveraging electrical control over non-classical surface effects.Comment: 10 pages, 3 figures, 15 pages Supplementar