~(13)C代谢通量分析

代谢通量分析(metabolic flux analysis,MFA)是通过确定代谢网络中代谢流分布来表征细胞代谢状态的强有力的工具。鉴于计量学代谢通量分析在处理复杂代谢网络时表现出的局限性,发展了以13C标记实验为基础的13C MFA。本文介绍了13C MFA的原理与方法,总结和评述了13C MFA在实验与数据分析方面的最新进展以及MFA在功能基因组研究中的重要地位,同时对代谢通量分析的发展前景进行了展望。     

Determination of Aqueous Nickel-Carbonate and Nickel-Oxalate Complexation Constants

An ion-exchange method was used to determine complexation constants for the Ni-oxalate and Ni-carbonate systems in a NaClO₄ background electrolyte. The Ni-oxalate data were interpreted in terms of a single Niox(aq) complex having log K ₁ values for Ni²⁺ + ox^2– Niox(aq) of 3.9 ± 0.1 (I.S. = 0.5 mol-L^–1 p[H] = 7.1) and 4.4 ± 0.1 (I.S. = 0.1 mol-L^–1 p[H] = 8.6) at 22 ± 1C. Specific ion-interaction theory (SIT) was used to obtain log K ₁ = 5.17 ± 0.05 (95% confidence level and = –0.23 ± 0.15) at I.S. = 0. The Ni-carbonate studies were carried out at p[H] values of 7.5, 8.5, and 9.6 in 0.5 mol-L^–1 NaClO₄/NaHCO₃ solutions. The NiCO₃(aq) species was the dominant complex in the [CO₃ ^2–] concentration ranges studied at all three p[H] values. A log K ₁ value for Ni²⁺ + CO₃ ^2– NiCO₃(aq) of 2.9 ± 0.3 was deduced at I.S. = 0.5 mol-L^–1. Extrapolating this value to zero ionic strength using the SIT approach yielded log K ₁ = 4.2 ± 0.3 (95% confidence level and = –0.26 ± 0.04). The data allowed upper bound values for the complexation constants for NiHCO₃ ⁺ and Ni(CO₃)₂ ^2– to be estimated, i.e., log K < 1.4 for Ni²⁺ + HCO₃ ^– NiHCO₃ ⁺, and log K ₂ < 2 for NiCO₃(aq) + CO₃ ^2– Ni(CO₃)₂ ^2–, respectively.     

Correlation of unified retention indices for OV-101 and squalane

Summary Gas chromatographic unified retention indices for 43 hydrocarbons (alkanes and cycloalkanes) are given for squalane and OV-101. Comparison of these values and unified retention index increments are presented as linear regression equations with high correlation coefficients and acceptable standard deviations.     

Multiple factor analysis in environmental chemistry

In environmental chemistry studies, it may be necessary to analyze data sets constituted by different blocks of variables, possibly of different types, measured on the same samples. Multiple factor analysis (MFA) is presented as a tool for exploring such data. The most important features of MFA are shown on a real environmental data set, consisting of two blocks of data, namely heavy metals and polycyclic aromatic hydrocarbons, measured for sediment samples. They are discussed and compared to principal component analysis (PCA). The usefulness of the weighting scheme used in MFA as a preprocessing step for other chemometric methods, such as clustering, is also highlighted.     

Gas chromatographic conditions for the linearity of the relationship between σT,t and tR in open tubes

The linearity of the relationship between σ_T,t² and (1 + k)² is studied with the view of using it for the evaluation of GC equipment. Based on appropriate analytical expressions it is concluded that in general this relationship is not linear and that practical procedures for column evaluation should be developed that take this non-linearity into account.     

Re-Evaluation of the Activity Coefficients of Aqueous Hydrochloric Acid Solutions up to a Molality of 2.0 Using Two-Parameter Hückel and Pitzer Equations. Part II. Results from 0 to 95°C

Simple two-parameter Hückel and Pitzer equations were used for the calculation of the activity coefficients of aqueous hydrochloric acid at temperatures 0–60°C up to a molality of 2.0 mol-kg^–1. The data obtained by Harned and Ehlers^(2,3) on galvanic cells without a liquid junction were used in the parameter estimations of these equations. These data consist of sets of measurements at the temperature intervals of 5°C. It was observed that all estimated parameters follow very simple equations with respect to temperature. They are either constant or depend linearly on the temperature. The values for the activity coefficient parameters calculated by these simple equations are recommended here. The recommended parameter values were tested by predicting the data of Gupta, Hills, and Ives,⁽⁵⁾ consisting of cell measurements from 5 to 45°C and molalities up to 1.0 mol-kg^–1, and the data of Bates and Bower,⁽⁴⁾ which extend to 95°C but measurements were only made on molalities less than about 0.1 mol-kg^–1. The activity coefficients obtained by the new equations were also compared to those calculated by the Pitzer equations with the parameter values determined by Saluja, Pitzer, and Phutela⁽⁶⁾ from calorimetric data. The agreement observed was excellent up to a molality of 1.5 mol-kg^–1 at temperatures from 0 to 60°C.     

Characterization and TG-MS studies of lactato and bipyridine-lactato complexes of Co(II) and Ni(II)

Two lactates and four new mixed ligand complexes with formulae Co(lact)₂·2H₂O, Ni(lact)₂·3H₂O, Co(4-bpy)(lact)₂, Co(2,4'-bpy)₂(lact)₂, Ni(4-bpy)(lact)₂·2H₂O and Ni(2,4'-bpy)₂(lact)₂ (where 4-bpy=4,4'-bipyridine, 2,4'-bpy=2,4'-bipyridine, lact=CH₃CH(OH)COO^-) were isolated and investigated. The thermal behaviour of compounds was studied by thermal analysis (TG, DTG, DTA). In the case of hydrated complexes thermal decomposition starts with the release of water molecules. The compounds decompose at high temperature to metal(II) oxides in air. A coupled TG-MS system was used to analyse the principal volatile products of thermolysis and fragmentation processes of obtained complexes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Topologisch und elektronisch bemerkenswerte „reduzierte”︁ Cluster des Typs [V18O42(X)]n− (X = SO4, VO4) mit Td-Symmetrie und davon abgeleitete Cluster [V(18–p)As2pO42(X)]m− (X = SO3, SO4, H2O; p = 3, 4)

Reduced Clusters with Remarkable Topological and Electronic Properties of the Type of [V₁₈O₄₂(X)]^n? (X = SO₄, VO₄) with T_d-Symmetry and Related Clusters [V_(18—p)As_2pO₄₂(X)]^m? (X = SO₃, SO₄, H₂O; p = 3, 4) The novel cluster-compounds Na₆[V₁₈O₄₂H₉(VO₄)] · 21 H₂O, (NH₄)₈[V₁₈O₄₂(SO₄)] · 25 H₂O, K₆[V₁₅As₆O₄₂(H₂O)] · 8 H₂O, (NH₄)₆[V₁₄As₈O₄₂(SO₃)], (NH₄)₆[V₁₄As₈O₄₂(SO₄)] and [N(CH3)₃]₄[₄V₁₄As₈0₄₂(H₂0)] were prepared and characterized by IR- and UV/Vis/NIR-spectroscopy, magnetic measurements and complete crystal structure analysis. For structural data see Inhaltsübersicht. Topological relations to the rhombicuboctahedron spanned by 24 0-atoms of the genuine hypothetical a-Keggin ion, at which the square planes are capped by V?O or As₂O groups, are discussed. Of particular interest are the ?extended”? Keggin ions [V₁₈O₄₂(X)]ⁿ- (X = SO₄ VO₄), (formaly derived from the hypothetical genuine a-Keggin ion by addition of six V?O groups) which have quite different electron populations in spite of the same structure of their cluster shells.     

A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: comparison with long-chain alpha-neurotoxins and alpha-conotoxins

Short-chain alpha-neurotoxins from snakes are highly selective antagonists of the muscle-type nicotinic acetylcholine receptors (nAChR). Although their spatial structures are known and abundant information on topology of binding to nAChR is obtained by labeling and mutagenesis studies, the accurate structure of the complex is not yet known. Here, we present a model for a short alpha-neurotoxin, neurotoxin II from Naja oxiana (NTII), bound to Torpedo californica nAChR. It was built by comparative modeling, docking and molecular dynamics using 1H NMR structure of NTII, cross-linking and mutagenesis data, cryoelectron microscopy structure of Torpedo marmorata nAChR [Unwin, N., 2005. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J. Mol. Biol. 346, 967-989] and X-ray structures of acetylcholine-binding protein (AChBP) with agonists [Celie, P.H., van Rossum-Fikkert, S.E., van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K., 2004. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures. Neuron 41 (6), 907-914] and antagonists: alpha-cobratoxin, a long-chain alpha-neurotoxin [Bourne, Y., Talley, T.T., Hansen, S.B., Taylor, P., Marchot, P., 2005. Crystal structure of Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors. EMBO J. 24 (8), 1512-1522] and alpha-conotoxin [Celie, P.H., Kasheverov, I.E., Mordvintsev, D.Y., Hogg, R.C., van Nierop, P., van Elk, R., van Rossum-Fikkert, S.E., Zhmak, M.N., Bertrand, D., Tsetlin, V., Sixma, T.K., Smit, A.B., 2005. Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant. Nat. Struct. Mol. Biol. 12 (7), 582-588]. In complex with the receptor, NTII was located at about 30 A from the membrane surface, the tip of its loop II plunges into the ligand-binding pocket between the alpha/gamma or alpha/delta nAChR subunits, while the loops I and III contact nAChR by their tips only in a 'surface-touch' manner. The toxin structure undergoes some changes during the final complex formation (for 1.45 rmsd in 15-25 ps according to AMBER'99 molecular dynamics simulation), which correlates with NMR data. The data on the mobility and accessibility of spin- and fluorescence labels in free and bound NTII were used in MD simulations. The binding process is dependent on spontaneous outward movement of the C-loop earlier found in the AChBP complexes with alpha-cobratoxin and alpha-conotoxin. Among common features in binding of short- and long alpha-neurotoxins is the rearrangement of aromatic residues in the binding pocket not observed for alpha-conotoxin binding. Being in general very similar, the binding modes of short- and long alpha-neurotoxins differ in the ways of loop II entry into nAChR.     

Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.