Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination

The high sensitivity of modern NMR instrumentation, in combination with full deuteration, enabled the measurement of long-range NOEs between amide protons in a fully deuterated protein corresponding to distances up to 8A. These are beyond the limit normally observed in protonated samples. Such long-distance NOEs could be observed using long mixing times, which became possible due to reduced spin diffusion and T1 relaxation of the amide protons in the fully deuterated sample. This information was used in combination with secondary structure restraints derived from secondary chemical shifts for structure calculations. With these backbone amide proton NOEs only, a unique fold could be obtained with positional root mean square deviations from the average of 1.30 and 2.25 A for backbone and heavy atoms, respectively. Despite the low density of restraints, no mirror image problems were observed. Addition of sidechain NOE information increased the precision of the ensemble and in particular of the core packing. The structures obtained in this way were close to the published crystal structure. NOE completeness analysis revealed that the cumulative completeness is still more than 80% for an 8.0 A cut-off distance.     

Wavenumber Calibration of CCD Detector Raman Spectrometers Controlled by a Sinus Arm Drive

Abstract

The calibration procedures needed for use of dispersive Raman spectrometers have been reviewed. Like other high‐precision spectrometers incorporating moving gratings, Raman spectrometers are subject to problems with wavenumber scale accuracy. Commercially available Raman spectrometers of types DILOR‐HORIBA LabRam and RENISHAW System 1000 have been examined for wavenumber scale stability, linearity, and reproducibility. For reliable use of the wavenumber data, daily calibration is a necessity. A procedure to examine the linearity of such mechanical drive systems is presented. A new finding was that the examined spectrometers give wavenumber calibration errors that were quite reproducible from day to day at a given temperature in the laboratory but depended markedly on the selected setting of the gratings. Knowledge of this linearity problem is essential for obtaining a reliable calibration. The most correct calibration was obtained by the use of certain “golden” settings of the sinus drive at a constant temperature of the laboratory. In this way, the examined spectrometers could be used with better precision, without daily calibration, provided the temperature of the room was constant or corrected for. A procedure for correction of these errors by the software is suggested.     

Using the natural 15N abundance to assess the main nitrogen inputs into the sand dune area of the North-Western Negev desert (ISRAEL)

The variation of the natural ¹⁵N abundance is often used to evaluate the origin of nitrogen or the pathways of N input into ecosystems. We tried to use this approach to assess the main input pathways of nitrogen into the sand dune area of the north-western Negev Desert (Israel). The following two pathways are the main sources for nitrogen input into the system:

1. Biological fixation of atmospheric nitrogen by cyanobacteria present in biological crusts and by N₂-fixing vascular plants (e.g. the shrub Retama raetam);

2. Atmospheric input of nitrogen by wet deposition with rainfall, dry deposition of dust containing N compounds, and gaseous deposition.

Samples were taken from selected environmental compartments such as biological crusts, sand underneath these crusts (down to a depth of 90?cm), N₂-fixing and non-N₂-fixing plants, atmospheric bulk deposition as well as soil from arable land north of the sandy area in three field campaigns in March 1998, 1999 and 2000. The δ¹⁵N values measured were in the following ranges: grass ?2.5‰ to +1.5‰; R. reatam: +0.5‰ to +4.5‰; non-N₂-fixing shrubs +1‰ to +7‰; sand beneath the biological crusts +4‰ to +20‰ (soil depth 2–90?cm); and arable land to the north up to 10‰. Thus, the natural ¹⁵N abundance of the different N pools varies significantly. Accordingly, it should be feasible to assess different input pathways from the various ¹⁵N abundances of nitrogen. For example, the biological N fixation rates of the Fabaceae shrub R. reatam from the ¹⁵N abundances measured were calculated to be 46–86% of biomass N derived from the atmosphere. The biological crusts themselves generally show slight negative ¹⁵N values (?3‰ to ?0.5‰), which can be explained by biological N fixation. However, areas with a high share of lichens, which are unable to fix atmospheric nitrogen, show very negative values down to ?10‰. The atmospheric N bulk deposition, which amounts to 1.9–3.8?kg?N/ha?yr, has a ¹⁵N abundance between 4.4‰ and 11.6‰ and is likely to be caused by dust from the arable land to the north. Thus, it cannot be responsible for the very negative values of lichens measured either. There must be an additional N input from the atmosphere with negative δ¹⁵N values, e.g. gaseous N forms (NO _x , NH₃). To explain these conflicting findings, detailed information is still needed on the wet, particulate and gaseous atmospheric deposition of nitrogen.     

BOLD responses to trigeminal nerve stimulation

The current study investigates a new model of barrel cortex activation using stimulation of the infraorbital branch of the trigeminal nerve. A robust and reproducible activation of the rat barrel cortex was obtained following trigeminal nerve stimulation. Blood oxygen level-dependent (BOLD) effects were obtained in the primary somatosensory barrel cortex (S1BF), the secondary somatosensory cortex (S2) and the motor cortex. These cortical areas were reached from afferent pathways from the trigeminal ganglion, the trigeminal nuclei and thalamic nuclei from which neurons project their axons upon whisker stimulation. The maximum BOLD responses were obtained for a stimulus frequency of 1 Hz, a stimulus pulse width of 100 μs and for current intensities between 1.5 and 3 mA. The BOLD response was nonlinear as a function of frequency and current intensity. Additionally, modeling BOLD responses in the rat barrel cortex from separate cerebral blood flow (CBF) and cerebral metabolic rate of oxygen (CMRO₂) measurements showed good agreement with the shape and amplitude of measured BOLD responses as a function of stimulus frequency and will potentially allow to identify the sources of BOLD nonlinearities. Activation of the rat barrel cortex using trigeminal nerve stimulation will contribute to the interpretation of the BOLD signals from functional magnetic resonance imaging studies.     

Cotangent functors of curve singularities

Let R be a complete analytic k-algebra of dimension one, where k is a field of characteristic 0. For a Noetherian normalization , the cotangent functors T_i(R/A, R) are of finite length. It is shown that if R is smoothable, then for all j, where denotes the complementary module. This result is used to give estimates for the length of the torsion of the module of differentials _R/k.     

Towards a finite element simulation of coating by means of thermal spraying

Metal sheet forming processes like deep drawing are applied in order to produce carriage parts in mass production. Therefore, forming tools are required that are well protected against wear. For such forming tools, wear resistant surfaces are, e.g., produced by thermal spraying of hard material coatings. The thermal spraying process itself is a highly transient thermo-mechanical process. In order to gain a better understanding of the heat input and transfer during thermal spraying, a simulation framework for thermal spraying processes is presented. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthetic and Biological Studies on New Urea and Triazole Containing Cystobactamid Derivatives

Cystobactamids belong to the group of arene-based oligoamides that effectively inhibit bacterial type IIa topoisomerases. Cystobactamid 861-2 is the most active member of these antibiotics. Most amide bonds present in the cystobactamids link benzoic acids with anilines and it was found that some of these amide bonds undergo chemical and enzymatic hydrolysis, especially the one linking ring C with ring D. This work reports on the chemical synthesis and biological evaluation of thirteen new cystobactamids that still contain the methoxyaspartate hinge. However, we exchanged selected amide bonds either by the urea or the triazole groups and modified ring A in the latter case. While hydrolytic stability could be improved with these structural substitutes, the high antibacterial potency of cystobactamid 861-2 could only be preserved in selected cases. This includes derivatives, in which the urea group is positioned between rings A and B and where the triazole is found between rings C and D.     

Packing of three copies of a graph

A graph of order n is said to be 3-placeable if there are three edge-disjoint copies of this graph in K_n. An (n, n − 1)-graph is a graph of order n with n − 1 edges. In this paper we characterize all the (n, n − 1)-graphs which contain no cycles of length 3 or 4 and which are 3-placeable. © 1996 John Wiley & Sons, Inc.     

Polymer membranes in medicine

Mass transfer within the human body primarily occurs across biological membranes. Medicine mimics nature and uses synthetic membranes for therapeutic purposes. The state of the art of polymer membrane applications in medicine is reviewed. The target for membrane material developments is mainly the improvement of the patients' safety and convenience. To provide optimal blood compatibility a new biocompatible polymer for hemodialysis membranes has been developed in our group: a polycarbonate with polyether blocks. The copolymer is suitable for production of membranes with excellent performance. In addition to therapeutic purposes polymer membranes can provide diagnostic functions. Recently a blood glucose test strip based on a synthetic membrane has been developed. The membrane separates off the erythrocytes and contains enzymes and reagents. It enables the diabetic a precise and convenient measurement.