Novel Tripod Amphiphiles for Membrane Protein Analysis

Integral membrane proteins play central roles in controlling the flow of information and molecules across membranes. Our understanding of membrane protein structures and functions, however, is seriously limited, mainly due to difficulties in handling and analysing these proteins in aqueous solution. The use of a detergent or other amphipathic agents is required to overcome the intrinsic incompatibility between the large lipophilic surfaces displayed by the membrane proteins in their native forms and the polar solvent molecules. Here, we introduce new tripod amphiphiles displaying favourable behaviours toward several membrane protein systems, leading to an enhanced protein solubilisation and stabilisation compared to both conventional detergents and previously described tripod amphiphiles.     

The BIOREMA project—part 3: International interlaboratory comparison for bio-ethanol test methods

The main objective of the reference materials for biofuel specifications (BIOREMA) project is the development of two test materials (one bio-ethanol material and one biodiesel material) with well-established reference values. Of a series of three papers, this part describes the material preparation, homogeneity study, stability study, and characterisation of the bio-ethanol material. The test material thus obtained was used in an interlaboratory comparison (ILC) to assess current practices and comparability amongst laboratories providing bio-ethanol testing services. Only 13 participants provided data, resulting in a small dataset for evaluation. Further, it appeared that for a number of laboratories, there was not sufficient material for the determination of all requested parameters. In most cases, as far as the data permit, it can be concluded that the consensus values (based on participant’s results) are in good agreement with the reference or the BIOREMA values (obtained by NMIs participating in the project). For three parameters, namely ethanol content, water content, and density, there is good agreement between the reference and consensus values. For these parameters, the reproducibility standard deviation is close to, or even smaller than, the expanded uncertainty associated with the reference value. A number of parameters show very poor reproducibility, for example, pH_e, electrolytic conductivity, and acidity. The same applies to sodium and copper content, which are very low and therefore challenging parameters to measure accurately. The results of the ILC underpin the need for certified reference materials and demonstrate the requirement for more robust quality control to improve the precision and trueness of the results from testing laboratories.     

Padé approximants for functions with branch points — strong asymptotics of Nuttall–Stahl polynomials

Let f be a germ of an analytic function at infinity that can be analytically continued along any path in the complex plane deprived of a finite set of points, \({f \in \mathcal{A}(\bar{\mathbb{C}} \setminus A)}\), \({\# A< \infty}\). J. Nuttall has put forward the important relation between the maximal domain of f where the function has a single-valued branch and the domain of convergence of the diagonal Padé approximants for f. The Padé approximants, which are rational functions and thus single-valued, approximate a holomorphic branch of f in the domain of their convergence. At the same time most of their poles tend to the boundary of the domain of convergence and the support of their limiting distribution models the system of cuts that makes the function f single-valued. Nuttall has conjectured (and proved for many important special cases) that this system of cuts has minimal logarithmic capacity among all other systems converting the function f to a single-valued branch. Thus the domain of convergence corresponds to the maximal (in the sense of minimal boundary) domain of single-valued holomorphy for the analytic function \({f\in\mathcal{A}(\bar{\mathbb{C}} \setminus A)}\). The complete proof of Nuttall’s conjecture (even in a more general setting where the set A has logarithmic capacity 0) was obtained by H. Stahl. In this work, we derive strong asymptotics for the denominators of the diagonal Padé approximants for this problem in a rather general setting. We assume that A is a finite set of branch points of f which have the algebro-logarithmic character and which are placed in a generic position. The last restriction means that we exclude from our consideration some degenerated “constellations” of the branch points.     

Edge Flips in Surface Meshes

Little theoretical work has been done on edge flips in surface meshes despite their popular usage in graphics and solid modeling to improve mesh equality. We propose the class of \((\varepsilon ,\alpha )\)-meshes of a surface that satisfy several properties: the vertex set is an \(\varepsilon \)-sample of the surface, the triangle angles are no smaller than a constant \(\alpha \), some triangle has a good normal, and the mesh is homeomorphic to the surface. We believe that many surface meshes encountered in practice are \((\varepsilon ,\alpha )\)-meshes or close to being one. We prove that flipping the appropriate edges can smooth a dense \((\varepsilon ,\alpha )\)-mesh by making the triangle normals better approximations of the surface normals and the dihedral angles closer to \(\pi \). Moreover, the edge flips can be performed in time linear in the number of vertices. This helps to explain the effectiveness of edge flips as observed in practice and in our experiments. A corollary of our techniques is that, in \(\mathbb {R}^2\), every triangulation with a constant lower bound on the angles can be flipped in linear time to the Delaunay triangulation.     

Simultaneous high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) analysis of cyanide and thiocyanate from swine plasma

An analytical procedure for the simultaneous determination of cyanide and thiocyanate in swine plasma was developed and validated. Cyanide and thiocyanate were simultaneously analyzed by high-performance liquid chromatography tandem mass spectrometry in negative ionization mode after rapid and simple sample preparation. Isotopically labeled internal standards, Na¹³C¹⁵N and NaS¹³C¹⁵N, were mixed with swine plasma (spiked and nonspiked), proteins were precipitated with acetone, the samples were centrifuged, and the supernatant was removed and dried. The dried samples were reconstituted in 10 mM ammonium formate. Cyanide was reacted with naphthalene-2,3-dicarboxaldehyde and taurine to form N-substituted 1-cyano[f]benzoisoindole, while thiocyanate was chemically modified with monobromobimane to form an SCN-bimane product. The method produced dynamic ranges of 0.1–50 and 0.2–50 μM for cyanide and thiocyanate, respectively, with limits of detection of 10 nM for cyanide and 50 nM for thiocyanate. For quality control standards, the precision, as measured by percent relative standard deviation, was below 8 %, and the accuracy was within ±10 % of the nominal concentration. Following validation, the analytical procedure successfully detected cyanide and thiocyanate simultaneously from the plasma of cyanide-exposed swine.     

Comprehensive and simultaneous coverage of lipid and polar metabolites for endogenous cellular metabolomics using HILIC-TOF-MS

The comprehensive metabolomic analyses using eukaryotic and prokaryotic cells are an effective way to identify biomarkers or biochemical pathways which can then be used to characterize disease states, differences between cell lines or inducers of cellular stress responses. One of the most commonly used extraction methods for comprehensive metabolomics is the Bligh and Dyer method (BD) which separates the metabolome into polar and nonpolar fractions. These fractions are then typically analysed separately using hydrophilic interaction liquid chromatography (HILIC) and reversed-phase (RP) liquid chromatography (LC), respectively. However, this method has low sample throughput and can also be biased to either polar or nonpolar metabolites. Here, we introduce a MeOH/EtOH/H₂O extraction paired with HILIC-time-of-flight (TOF)-mass spectrometry (MS) for comprehensive and simultaneous detection of both polar and nonpolar metabolites that is compatible for a wide array of cellular species cultured in different growth media. This method has been shown to be capable of separating polar metabolites by a HILIC mechanism and classes of lipids by an adsorption-like mechanism. Furthermore, this method is scalable and offers a substantial increase in sample throughput compared to BD with comparable extraction efficiency. This method was able to cover 92.2 % of the detectable metabolome of Gram-negative bacterium Sinorhizobium meliloti, as compared to 91.6 % of the metabolome by a combination of BD polar (59.4 %) and BD nonpolar (53.9 %) fractions. This single-extraction HILIC approach was successfully used to characterize the endometabolism of Gram-negative and Gram-positive bacteria as well as mammalian macrophages.

Rapid and simple electrochemical detection of morphine on graphene–palladium-hybrid-modified glassy carbon electrode

A hybrid of reduced graphene oxide–palladium (RGO–Pd) nano- to submicron-scale particles was simultaneously chemically prepared using microwave irradiation. The electrochemical investigation of the resulting hybrid was achieved using cyclic voltammetry and differential pulse voltammetry. RGO–Pd had a higher current response than unmodified RGO toward the oxidation of morphine. Several factors that can affect the electrochemical response were studied, including accumulation time and potential, Pd loading, scan rate, and pH of electrolyte. At the optimum conditions, the concentration of morphine was determined using differential pulse voltammetry in a linear range from 0.34 to 12 μmol L^?1 and from 14 to 100 μmol L^?1, with detection limits of 12.95 nmol L^?1 for the first range. The electrode had high sensitivity toward morphine oxidation in the presence of dopamine (DA) and of the interference compounds ascorbic acid (AA) and uric acid (UA). Electrochemical determination of morphine in a spiked urine sample was performed, and a low detection limit was obtained. Validation conditions including reproducibility, sensitivity, and recovery were evaluated successfully in the determination of morphine in diluted human urine.

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Simulation of oxidative stress of guanosine and 8-oxo-7,8-dihydroguanosine by electrochemically assisted injection–capillary electrophoresis–mass spectrometry

Oxidative stress plays a crucial role in DNA and RNA damage within biological cells. As a consequence, mutations of DNA can occur, leading to disorders like cancer and neurodegenerative and cardiovascular diseases. The oxidative attack of guanosine and 8-oxo-7,8-dihydroguanosine is simulated by electrochemistry coupled to capillary electrophoresis–mass spectrometry. The electrochemical conversion of the compound of interest is implemented in the injection protocol termed electrochemically assisted injection (EAI). In this way, oxidation products of guanosine can be generated electrochemically, separated by capillary electrophoresis, and detected by electrospray ionization time-of-flight mass spectrometry (EAI–CE–MS). A fully automated laboratory-made EAI cell with an integrated buffer reservoir and a compartment holding screen-printed electrodes is used for the injection. In this study, parameters like pH of the sample solution and the redox potential applied during the injection were investigated in terms of corresponding formation of well-known markers of DNA damage. The important product species, 8-oxo-7,8-dihydroguanosine, was investigated in a separate study to distinguish between primary and secondary oxidation products. A comparison of product species formed under alkaline, neutral, and acidic conditions is presented. To compare real biological systems with an analytical approach for simulation of oxidative stress, it is desirable to have a well-defined control over the redox potential and to use solutions, which are close to physiological conditions. In contrast to typical HPLC–MS protocols, the hyphenation of EAI, CE, and MS enables the generation and separation of species involved without the use of organic solvents. Thus, information of the electrochemical behavior of the nucleoside guanosine as well as the primary oxidation product 8-oxo-7,8-dihydroguanosine can be characterized under conditions close to the physiological situation. In addition, the migration behavior found in CE separations of product species can be used to identify compounds if several possible species have the same mass-to-charge values determined by MS detection.

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Poly (methyl methacrylate) grafted wheat straw for economical and eco-friendly treatment of oily wastewater

Cellulose - The sustainable development of oil–gas and petrochemical industries necessitates the development of cost-effective and eco-friendly technologies to treat mass-produced oily...