Mono‐, di‐ and trimethylated homologues of isoprenoid tetraether lipid cores in archaea and environmental samples: mass spectrometric identification and significance

Higher homologues of widely reported C₈₆ isoprenoid diglycerol tetraether lipid cores, containing 0–6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography‐tandem mass spectrometry confirms that the additional carbon atoms in the C_87‐88 homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl (‘H‐shaped’) tetraethers containing C_40‐42 or C_81‐82 hydrocarbons, respectively, many representing novel compounds. Gas chromatography‐mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C₄₀ chains are biphytanes and the C₄₁ chains 13‐methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments from geographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di‐ and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C_87‐89 tetraethers highlight their potential as complementary biomarkers for archaea in natural environments. Copyright © 2015 John Wiley & Sons, Ltd.     

A Multi‐Addressable Switch Based on the Dimethyldihydropyrene Photochrome with Remarkable Proton‐Triggered Photo‐opening Efficiency

A series of photochromic derivatives based on the trans‐10b,10c‐dimethyl‐10b,10c‐dihydropyrene (DHP, “closed form”) skeleton has been synthesized and their photoisomerization leading to the corresponding cyclophanediene (CPD, “open form”) isomers has been investigated by UV/Vis and ¹H NMR spectroscopies. Substitution of the DHP core with electron‐withdrawing pyridinium groups was found to have major effects on the photoisomerization efficiency, the most remarkable examples being to enhance the quantum yield of the opening reaction and to allow fast and quantitative conversions at much lower radiant energies. This effect was rationalized by theoretical calculations. We also show that the reverse reaction, that is, going from the open form to the closed form, can be electrochemically triggered by oxidation of the CPD unit and that the photo‐opening properties of pyridine‐substituted DHPs can be efficiently tuned by protonation, the system behaving as a multi‐addressable molecular switch. These multi‐addressable photochromes show promise for the development of responsive materials.     

Generalizing the ENO-DB2<Emphasis Type="Italic">p</Emphasis> transform using the inverse wavelet transform

The essentially non-oscillatory (ENO)-wavelet transform developed by Chan and Zhou (SIAM J. Numer. Anal. 40(4), 1369–1404, 2002) is based on a combination of the Daubechies-2p wavelet transform and the ENO technique. It uses extrapolation methods to compute the scaling coefficients without differencing function values across jumps and obtains a multiresolution framework (essentially) free of edge artifacts. In this work, we present a different way to compute the ENO-DB2p wavelet transform of Chan and Zhou which allows us to simplify the process and easily generalize it to other families of orthonormal wavelets.     

Brownian Paths Homogeneously Distributed in Space: Percolation Phase Transition and Uniqueness of the Unbounded Cluster

We consider a continuum percolation model on \(\mathbb {R}^d\), \(d\ge 1\). For \(t,\lambda \in (0,\infty )\) and \(d\in \{1,2,3\}\), the occupied set is given by the union of independent Brownian paths running up to time t whose initial points form a Poisson point process with intensity \(\lambda >0\). When \(d\ge 4\), the Brownian paths are replaced by Wiener sausages with radius \(r>0\). We establish that, for \(d=1\) and all choices of t, no percolation occurs, whereas for \(d\ge 2\), there is a non-trivial percolation transition in t, provided \(\lambda \) and r are chosen properly. The last statement means that \(\lambda \) has to be chosen to be strictly smaller than the critical percolation parameter for the occupied set at time zero (which is infinite when \(d\in \{2,3\}\), but finite and dependent on r when \(d\ge 4\)). We further show that for all \(d\ge 2\), the unbounded cluster in the supercritical phase is unique. Along the way a finite box criterion for non-percolation in the Boolean model is extended to radius distributions with an exponential tail. This may be of independent interest. The present paper settles the basic properties of the model and should be viewed as a springboard for finer results.     

A Sharp Upper Bound for the¶Torsional Rigidity of Rods¶by Means of Web Functions

Using web functions, we approximate the Dirichlet integral which represents the torsional rigidity of a cylindrical rod with planar convex cross-section Ω. To this end, we use a suitably defined piercing function, which enables us to obtain bounds for both the approximate and the exact value of the torsional rigidity. When Ω varies, we show that the ratio between these two values is always larger than ¾; we prove that this is a sharp lower bound and that it is not attained. Several extremal cases are also analyzed and studied by numerical methods.     

Isothermal titration calorimetry of Ni(II) binding to histidine and to N-2-aminoethylglycine

Isothermal titration calorimetry (ITC) is used to study the complexation thermodynamics of Ni(II) with histidine (His) and with N-2-aminoethylglycine (EDMA). The titrations were performed in HEPES and Tris buffers at various ionic strengths and pH values around 8. The results show the influence of the experimental conditions on the shape and fitting parameters of the calorimetric curves. For the studied systems, the main reaction is concomitant with a number of side reactions which contribute to the global energy measured. From the calorimetric data measured, the formation constants for the species NiHEPES⁺, Tris⁺His⁻, TrisNiHis⁺ and [Ni(EDMA)₂OH]⁻ have been evaluated for the first time and the values obtained properly validated.     

Aβ40 and Aβ42 amyloid fibrils exhibit distinct molecular recycling properties

A critical aspect to understanding the molecular basis of Alzheimer's disease (AD) is the characterization of the kinetics of interconversion between the different species present during amyloid-β protein (Aβ) aggregation. By monitoring hydrogen/deuterium exchange in Aβ fibrils using electrospray ionization mass spectrometry, we demonstrate that the Aβ molecules comprising the fibril continuously dissociate and reassociate, resulting in molecular recycling within the fibril population. Investigations on Aβ40 and Aβ42 amyloid fibrils reveal that molecules making up Aβ40 fibrils recycle to a much greater extent than those of Aβ42. By examining factors that could influence molecular recycling and by running simulations, we show that the rate constant for dissociation of molecules from the fibril (k(off)) is much greater for Aβ40 than that for Aβ42. Importantly, the k(off) values obtained for Aβ40 and Aβ42 reveal that recycling occurs on biologically relevant time scales. These results have implications for understanding the role of Aβ fibrils in neurotoxicity and for designing therapeutic strategies against AD.     

Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics

Riboswitches regulate gene expression via specific recognition of cognate metabolites by their aptamer domains, which fold into stable conformations upon ligand binding. However, the recently reported solution and crystal structures of the Bacillus subtilis preQ(1) riboswitch aptamer show small but significant differences, suggesting that there may be conformational heterogeneity in the ligand-bound state. We present a structural and dynamic characterization of this aptamer by solution NMR spectroscopy. The aptamer-preQ(1) complex is intrinsically flexible in solution, with two regions that undergo motions on different time scales. Three residues move in concert on the micro-to-millisecond time scale and may serve as the lid of the preQ(1)-binding pocket. Several Ca(2+) ions are present in the crystal structure, one of which binds with an affinity of 47 ± 2 μM in solution to a site that is formed only upon ligand binding. Addition of Ca(2+) to the aptamer-preQ(1) complex in solution results in conformational changes that account for the differences between the solution and crystal structures. Remarkably, the Ca(2+) ions present in the crystal structure, which were proposed to be important for folding and ligand recognition, are not required for either in solution.     

(Liquid + liquid) equilibrium for the ternary systems {heptane + toluene + 1-allyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide} and {heptane + toluene + 1-methyl-3-propylimidazolium bis(trifluoromethylsulfonyl)imide} ionic liquids

The (liquid + liquid) equilibrium (LLE) data for two systems containing heptane, toluene, and 1-methyl-3-propylimidazolium bis(trifluoromethylsulfonyl)imide ([mpim][Tf₂N]) or 1-allyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([amim][Tf₂N]) ionic liquids (ILs) were determined at T = 313.2 K and atmospheric pressure. The effect of a double bond in an alkyl side chain in the imidazolium cation was evaluated in terms of selectivity and extractive capacity. The results show a decrease of the amount of toluene and heptane dissolved in the IL with the allyl group. Thus, the distribution ratios of toluene and heptane of [mpim][Tf₂N] IL are higher than those of [amim][Tf₂N] IL. On the other hand, the separation factor of the [amim][Tf₂N] IL increases comparing to [mpim][Tf₂N] IL. The NRTL model was used to correlate satisfactorily the experimental LLE data for the two studied ternary systems.