A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection

The calculation of projection structures (PSs) from Protein Data Bank (PDB)-coordinate files of membrane proteins is not well-established. Reports on such attempts exist but are rare. In addition, the different procedures are barely described and thus difficult if not impossible to reproduce. Here we present a simple, fast and well-documented method for the calculation and visualization of PSs from PDB-coordinate files of membrane proteins: the projection structure visualization (PSV)-method. The PSV-method was successfully validated using the PS of aquaporin-1 (AQP1) from 2D crystals and cryo-transmission electron microscopy, and the PDB-coordinate file of AQP1 determined from 3D crystals and X-ray crystallography. Besides AQP1, which is a relatively rigid protein, we also studied a flexible membrane transport protein, i.e. the L-arginine/agmatine antiporter AdiC. Comparison of PSs calculated from the existing PDB-coordinate files of substrate-free and L-arginine-bound AdiC indicated that conformational changes are detected in projection. Importantly, structural differences were found between the PSV-method calculated PSs of the detergent-solubilized AdiC proteins and the PS from cryo-TEM of membrane-embedded AdiC. These differences are particularly exciting since they may reflect a different conformation of AdiC induced by the lateral pressure in the lipid bilayer.

Exploratory studies on coordination chemistry of a redox-active bridging ligand: synthesis, properties and solid state structures of the complexes

The explorative coordination chemistry of the bridging ligand TTF-PPB is presented. Its strong binding ability to Co(II) and then to Ni(II) or Cu(II) in the presence of hexafluoroacetylacetonate (hfac(-)), forming new mono-and dinuclear complexes 1-3, is described. X-ray crystallographic studies have been conducted in the case of the free ligand TTF-PPB as well as its complexes [Co(TTF-PPB)(hfac)(2)] (1) and [Co(hfac)(2)(mu-TTF-PPB)Ni(hfac)(2)] (2). Each metal ion is bonded to two bidentate hfac-anions through their oxygen atoms and two nitrogen atoms of the PPB moiety with a distorted octahedral coordination geometry. Specifically, nitrogen donor atoms of TTF-PPB adopt a cis-coordination but not in the equatorial plane, which is quite rare. Electronic absorption, photoinduced intraligand charge transfer ((1)ILCT), and electrochemical behaviour of 1-3 have been investigated. UV-Vis spectroscopy shows very strong bands in the UV region consistent with ligand centred pi-pi* transitions and an intense broad band in the visible region corresponding to a spin-allowed pi-pi* (1)ILCT transition. Upon coordination, the (1)ILCT band is bathochromically shifted by 3100, 6100 and 5900 cm(-1) on going from 1 to 3. The electrochemical studies reveal that all of them undergo two reversible oxidation and one reversible reduction processes, ascribed to the successive oxidations of the TTF moiety and the reduction of the PPB unit, respectively.

Interactions of nanoparticles with pulmonary structures and cellular responses

Combustion-derived and synthetic nano-sized particles (NSP) have gained considerable interest among pulmonary researchers and clinicians for two main reasons: 1) Inhalation exposure to combustion-derived NSP was associated with increased pulmonary and cardiovascular morbidity and mortality as suggested by epidemiological studies. Experimental evidence has provided a mechanistic picture of the adverse health effects associated with inhalation of combustion-derived and synthetic NSP. 2) The toxicological potential of NSP contrasts with the potential application of synthetic NSP in technological as well as medicinal settings with the latter including the use of NSP as diagnostics or therapeutics. In order to shed light on this paradox, this article aims to highlight recent findings about the interaction of inhaled NSP with the structures of the respiratory tract including surfactant and alveolar macrophages and epithelial cells. Cellular responses to NSP exposure include the generation of reactive oxygen species and the induction of an inflammatory response. Furthermore, this review places special emphasis on methodological differences between experimental studies and the caveats associated with the dose metrics and points out ways to overcome inherent methodological problems. Key words: electron tomography, surfactant, translocation, oxidative stress, inflammation.

Two-dimensional assembly and local redox-activity of molecular hybrid structures in an electrochemical environment

The self-assembly and redox-properties of two viologen derivatives, N-hexyl-N-(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-H) and N,N-bis(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-SH), immobilized on Au(111)-(1x1) macro-electrodes were investigated by cyclic voltammetry, surface enhanced infrared spectroscopy (SEIRAS) and in situ scanning tunneling microscopy (STM). Depending on the assembly conditions one could distinguish three different types of adlayers for both viologens: a low coverage disordered and an ordered striped phase of flat oriented molecules as well as a high coverage monolayer composed of tilted viologen moieties. Both molecules, HS-6V6-H and HS-6V6-SH, were successfully immobilized on Au(poly) nano-electrodes, which gave a well-defined redox-response in the lower pA–current range. An in situ STM configuration was employed to explore electron transport properties of single molecule junctions Au(T)|HS-6V6-SH(HS-6V6-H)|Au(S). The observed sigmoidal potential dependence, measured at variable substrate potential ES and at constant bias voltage (ET–ES), was attributed to electronic structure changes of the viologen moiety during the one-electron reduction/re-oxidation process V2+ V+. Tunneling experiments in asymmetric, STM-based junctions Au(T)-S-6V6-H|Au(S) revealed current (iT)–voltage (ET) curves with a maximum located at the equilibrium potential of the redox-process V2+ V+. The experimental iT–ET characteristics of the HS-6V6-H–modified tunneling junction were tentatively attributed to a sequential two-step electron transfer mechanism.

New copper(II) complexes with isoconazole: Synthesis, structures and biological properties

There is an increasing demand for novel metal-based complexes with biologically relevant molecules in technology and medicine. Three new Cu(II) coordination compounds with antifungal agent isoconazole (L), namely mononuclear complexes CuCl2(L)(2) (1), and Cu(O2CMe)(2)(L)(2)center dot 2H(2)O (2) and coordination polymer Cu(pht)(L)(2)(n) (3) (where H(2)pht - o-phthalic acid) were synthesized and characterized by IR spectroscopy, thermogravimetric analysis and X-ray crystallography. X-ray analysis showed that in all complexes, the isoconazole is coordinated to Cu(II) centres by a N atom of the imidazole fragment. In complex I, the square-planar environment of Cu(II) atoms is completed by two N atoms of isoconazole and two chloride ligands, whereas the Cu(II) atoms are coordinated by two N atoms from two isoconazole ligands and two O atoms from the different carboxylate residues: acetate in 2 and phthalate in 3. The formation of an infinite chain through the bridging phthalate ligand is observed in 3. The biosynthetic ability of micromycetes Aspergillus niger CNMN FD 10 in the presence of the prepared complexes 1-3 as well as the antifungal drug isoconazole were studied. Complexes 2 and 3 accelerate the biosynthesis of enzymes (beta-glucosidase, xylanase and endoglucanase) by this fungus. Moreover, a simplified and improved method for the preparation of isoconazole nitrate was developed.

Past forest composition, structures and processes – How paleoecology can contribute to forest conservation

The importance of long-term historical information derived from paleoecological studies has long been recognized as a fundamental aspect of effective conservation. However, there remains some uncertainty regarding the extent to which paleoecology can inform on specific issues of high conservation priority, at the scale for which conservation policy decisions often take place. Here we review to what extent the past occurrence of three fundamental aspects of forest conservation can be assessed using paleoecological data, with a focus on northern Europe. These aspects are (1) tree species composition, (2) old/large trees and coarse woody debris, and (3) natural disturbances. We begin by evaluating the types of relevant historical information available from contemporary forests, then evaluate common paleoecological techniques, namely dendrochronology, pollen, macrofossil, charcoal, and fossil insect and wood analyses. We conclude that whereas contemporary forests can be used to estimate historical, natural occurrences of several of the aspects addressed here (e.g. old/large trees), paleoecological techniques are capable of providing much greater temporal depth, as well as robust quantitative data for tree species composition and fire disturbance, qualitative insights regarding old/large trees and woody debris, but limited indications of past windstorms and insect outbreaks. We also find that studies of fossil wood and paleoentomology are perhaps the most underutilized sources of information. Not only can paleoentomology provide species specific information, but it also enables the reconstruction of former environmental conditions otherwise unavailable. Despite the potential, the majority of conservation-relevant paleoecological studies primarily focus on describing historical forest conditions in broad terms and for large spatial scales, addressing former climate, land-use, and landscape developments, often in the absence of a specific conservation context. In contrast, relatively few studies address the most pressing conservation issues in northern Europe, often requiring data on the presence or quantities of dead wood, large trees or specific tree species, at the scale of the stand or reserve. Furthermore, even fewer examples exist of detailed paleoecological data being used for conservation planning, or the setting of operative restorative baseline conditions at local scales. If ecologist and conservation biologists are going to benefit to the full extent possible from the ever-advancing techniques developed by the paleoecological sciences, further integration of these disciplines is desirable.

Changing correlation structures of the Northern Hemisphere atmospheric circulation from 1000 to 2100 AD

Atmospheric circulation modes are important concepts in understanding the variability of atmospheric dynamics. Assuming their spatial patterns to be fixed, such modes are often described by simple indices from rather short observational data sets. The increasing length of reanalysis products allows these concepts and assumptions to be scrutinised. Here we investigate the stability of spatial patterns of Northern Hemisphere teleconnections by using the Twentieth Century Reanalysis as well as several control and transient millennium-scale simulations with coupled models. The observed and simulated centre of action of the two major teleconnection patterns, the North Atlantic Oscillation (NAO) and to some extent the Pacific North American (PNA), are not stable in time. The currently observed dipole pattern of the NAO, its centre of action over Iceland and the Azores, split into a north–south dipole pattern in the western Atlantic with a wave train pattern in the eastern part, connecting the British Isles with West Greenland and the eastern Mediterranean during the period 1940–1969 AD. The PNA centres of action over Canada are shifted southwards and over Florida into the Gulf of Mexico during the period 1915–1944 AD. The analysis further shows that shifts in the centres of action of either teleconnection pattern are not related to changes in the external forcing applied in transient simulations of the last millennium. Such shifts in their centres of action are accompanied by changes in the relation of local precipitation and temperature with the overlying atmospheric mode. These findings further undermine the assumption of stationarity between local climate/proxy variability and large-scale dynamics inherent when using proxy-based reconstructions of atmospheric modes, and call for a more robust understanding of atmospheric variability on decadal timescales.

Measuring the bending of asymmetric planar EAP structures

The geometric characterization of low-voltage dielectric electro-active polymer (EAP) structures, comprised of nanometer thickness but areas of square centimeters, for applications such as artificial sphincters requires methods with nanometer precision. Direct optical detection is usually restricted to sub-micrometer resolution because of the wavelength of the light applied. Therefore, we propose to take advantage of the cantilever bending system with optical readout revealing a sub-micrometer resolution at the deflection of the free end. It is demonstrated that this approach allows us to detect bending of rather conventional planar asymmetric, dielectric EAP-structures applying voltages well below 10 V. For this purpose, we built 100 μm-thin silicone films between 50 nm-thin silver layers on a 25 μm-thin polyetheretherketone (PEEK) substrate. The increase of the applied voltage in steps of 50 V until 1 kV resulted in a cantilever bending that exhibits only in restricted ranges the expected square dependence. The mean laser beam displacement on the detector corresponded to 6 nm per volt. The apparatus will therefore become a powerful mean to analyze and thereby improve low-voltage dielectric EAP-structures to realize nanometer-thin layers for stack actuators to be incorporated into artificial sphincter systems for treating severe urinary and fecal incontinence.

Coalition Structures and Policy Change in a Consensus Democracy

This paper studies the relation between coalition structures in policy processes and policy change. While different factors such as policy images, learning processes, external events, or venue shopping are important to explain policy change, coalition structures within policy processes are often neglected. However, policy change happens as a result of negotiations and coordination among coalitions within policy processes. The paper analyzes how conflict, collaboration, and power relations among coalitions of actors influence policy change in an institutional context of a consensus democracy. Empirically, I rely on a Qualitative Comparative Analysis to conduct a cross-sector comparison of the 11 most important policy processes in Switzerland between 2001 and 2006. Coalition structures with low conflict and strong collaboration among coalitions as well as structures with dominant coalitions and weak collaboration both facilitate major policy change. Competing coalitions that are separated by strong conflict but still collaborate strongly produce policy outputs that are close to the status quo.

Nickel(II)-, cobalt(II)-, copper(II)-, and zinc(II)-phthalate and 1-methylimidazole coordination compounds: synthesis, crystal structures and magnetic properties

Three new coordination polymers [M(Pht)(1-MeIm)2]n (where M=Cu (1), Zn (2), Co (3); Pht2−=dianion of o-phthalic acid; 1-MeIm=1-methylimidazole) and two compounds [M(1-MeIm)6](HPht)2 · 2H2O (M=Co (4), Ni (5)) have been synthesized and characterized by X-ray crystallography. The structures of 1–3 (2 is isostructural to 3) consist of [M(1-MeIm)2] building units connected by 1,6-bridging phthalate ions to form infinite chains. In complex 1, each copper(II) center adopts a square coordination mode of N2O2 type by two O atoms from different phthalate ions and two N atoms of 1-MeIm, whereas in 3 two independent metal atoms are tetrahedrally (N2O2) coordinated to a pair of Pht ligands and a pair of 1-MeIm molecules. There are only van der Waals interactions between the chains in 1, while the three-dimensional network in 3 is assembled by C–H⋯O contacts. In contrast to polymers 1–3 the structures of 4 and 5 (complexes are also isostructural) are made up of the [M(1-MeIm)6]2+ cation, two hydrogen phthalate anions (HPht−) and two H2O solvate molecules. The coordination around each metal(II) atom is octahedral with six nitrogen atoms of 1-MeIm. Extended hydrogen bonding networks embracing the solvate water molecules and a phthalate residue as well as the weak C–H⋯O interactions stabilize the three-dimensional structures. Magnetic studies clearly show that the magnetic ions do not interact with each other. Furthermore, in compound 4 we have another example of a highly anisotropic Co2+ ion with a rhombic g-tensor and large zero-field-splitting. The complexes were also characterized by IR and 1H NMR spectroscopy, thermogravimetric analysis, and all data are discussed in the terms of known structures.

Automatic multi-resolution shape modeling of multi-organ structures.

Point Distribution Models (PDM) are among the most popular shape description techniques and their usefulness has been demonstrated in a wide variety of medical imaging applications. However, to adequately characterize the underlying modeled population it is essential to have a representative number of training samples, which is not always possible. This problem is especially relevant as the complexity of the modeled structure increases, being the modeling of ensembles of multiple 3D organs one of the most challenging cases. In this paper, we introduce a new GEneralized Multi-resolution PDM (GEM-PDM) in the context of multi-organ analysis able to efficiently characterize the different inter-object relations, as well as the particular locality of each object separately. Importantly, unlike previous approaches, the configuration of the algorithm is automated thanks to a new agglomerative landmark clustering method proposed here, which equally allows us to identify smaller anatomically significant regions within organs. The significant advantage of the GEM-PDM method over two previous approaches (PDM and hierarchical PDM) in terms of shape modeling accuracy and robustness to noise, has been successfully verified for two different databases of sets of multiple organs: six subcortical brain structures, and seven abdominal organs. Finally, we propose the integration of the new shape modeling framework into an active shape-model-based segmentation algorithm. The resulting algorithm, named GEMA, provides a better overall performance than the two classical approaches tested, ASM, and hierarchical ASM, when applied to the segmentation of 3D brain MRI.

Bone conduction responses of middle ear structures in Thiel embalmed heads

Thiel-embalmed human whole-head specimens offer a promising alternative model for bone conduction (BC) studies of middle ear structures. In this work we present the Thiel model’s linearity and stability over time as well as its possible use in the study of a fixed ossicle chain. Using laser Doppler vibrometry (LDV), the motion of the retroauricular skull, the promontory, the stapes footplate and the round window (RW) were measured. A bone-anchored hearing aid stimulated the ears with step sinus tones logarithmically spread between 0.1 and 10 kHz. Linearity of the model was verified using input levels in steps of 10 dBV. The stability of the Thiel model over time was examined with measurements repeated after hours and weeks. The influence of a cement-fixed stapes was assessed. The middle ear elements measured responded linearly in amplitude for the applied input levels (100, 32.6, and 10 mV). The variability of measurements for both short- (2 h) and long-term (4-16 weeks) repetitions in the same ear was lower than the interindividual difference. The fixation of the stapes induced a lowered RW displacement for frequencies near 750 Hz (-4 dB) and an increased displacement for frequencies above 1 kHz (max. +3.7 dB at 4 kHz). LDV assessment of BC-induced middle ear motion in Thiel heads can be performed with stable results. The vibratory RW response is affected by the fixation of the stapes, indicating a measurable effect of ossicle chain inertia on BC response in Thiel embalmed heads.