Towards validating a method for two-dimensional electrophoresis/silver staining

Two-dimensional electrophoresis (2-DE) is a technique involving numerous steps, many of them to be performed manually. Hence, some operator dependency must be taken into account. An attempt to elucidate the reliability of 2-DE combined with silver staining is presented, employing the general practice to validate a method in pharmaceutical analysis. Most proteomic studies employing 2-DE aim at qualitative or quantitative differences in protein expression. One of the most sensitive and broadly applied staining techniques is silver staining. In order to gain information on accuracy, precision, linearity, and ruggedness of this technique, gels were run in replicates with different amounts of protein from a complex standard sample. In addition, sets of gels were repeated by two different operators in a second independent laboratory equipped with identical hardware and software. Our results show that reliable qualitative data on differential protein expression can be obtained by 2-DE, nevertheless replicate gels should be run and experimental conditions have to be kept stringently to a standardized protocol. Quantitative data are just achievable with spots, which are well-resolved, of high quality, with an optical density (OD) above a certain threshold (OD > 10), and which show a linear response. Quantitative differences occurring due to method-derived deviations may easily be misinterpreted as true changes in protein expression. After normalization, relative standard deviation (RSD) values of approximately 30% (n = 4) could be obtained, therefore minor changes (< 50%) should be critically reviewed.     

[Cs6Cl][Fe24Se26]: A Host–Guest Compound with Unique Fe–Se Topology

The novel host–guest compound [Cs₆Cl][Fe₂₄Se₂₆] (I4/mmm; a=11.0991(9), c=22.143(2) Å) was obtained by reacting Cs₂Se, CsCl, Fe, and Se in closed ampoules. This is the first member of a family of compounds with unique Fe–Se topology, which consists of edge‐sharing, extended fused cubane [Fe₈Se₆Se_8/3] blocks that host a guest complex ion, [Cs₆Cl]⁵⁺. Thus Fe is tetrahedrally coordinated and divalent with strong exchange couplings, which results in an ordered antiferromagnetic state below T_N=221 K. At low temperatures, a distribution of hyperfine fields in the Mössbauer spectra suggests a structural distortion or a complex spin structure. With its strong Fe–Se covalency, the compound is close to electronic itinerancy and is, therefore, prone to exhibit tunable properties.     

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

The redox activity of cysteine sulfur allows numerous post‐translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas‐phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSO_x]^? (x=1, 2, 3, representing the number of S‐bound oxygen atoms), which are key intermediates in the redox‐switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur‐containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO^? in [cysSO]^? migrates to the carboxylate in [cysSO₃]^?, whereas it turns out to be shared in [cysSO₂]^?. Evidence is gathered that a mixture of close‐lying low‐energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.     

Characterisation of regioselectively functionalized 2,3-O-carboxymethyl cellulose by enzymatic and chemical methods

The determination of the molecular structure of 2,3-O-carboxymethyl cellulose (2,3-O-CMC), prepared via 6-O-(4-monomethoxy)triphenylmethyl cellulose, was carried out in detail by means of enzymatic and chemical methods. The 2,3-O-CMCs had degrees of substitution (DS) in the range of 0.5–1.2 showing a narrow molar mass distribution as revealed by SEC. As a result of an endoglucanase treatment, an intensive depolymerization of the samples occurred which was more pronounced for 2,3-O-CMC with comparatively low DS. All degraded samples could be separated into 18 fractions by preparative SEC and the proportion of each individual repeat unit was analysed by anion exchange chromatography (AEC) following complete hydrolytic chain degradation. The results indicated a homogeneous distribution of the functional groups within the polymer chain. Moreover, it became obvious that a preferred carboxymethylation of O-2 compared with O-3 occurred and that a preferred functionalization of already carboxymethylated units occurred as the reaction progressed. AEC with pulsed amperometric detection, which was used to separate and analyse the differently functionalized repeating units as well as glucose, had to be calibrated. Therefore, a method to determine the response factors of the individual carboxymethylated glucose units was developed using ¹³C NMR spectroscopic measurements (inverse gated decoupling) of depolymerised 2,3-O-CMC.     

Minimum-weight cycle covers and their approximability

A cycle cover of a graph is a set of cycles such that every vertex is part of exactly one cycle. An L-cycle cover is a cycle cover in which the length of every cycle is in the set L⊆N.We investigate how well L-cycle covers of minimum weight can be approximated. For undirected graphs, we devise non-constructive polynomial-time approximation algorithms that achieve constant approximation ratios for all sets L. On the other hand, we prove that the problem cannot be approximated with a factor of 2−ε for certain sets L.For directed graphs, we devise non-constructive polynomial-time approximation algorithms that achieve approximation ratios of O(n), where n is the number of vertices. This is asymptotically optimal: We show that the problem cannot be approximated with a factor of o(n) for certain sets L.To contrast the results for cycle covers of minimum weight, we show that the problem of computing L-cycle covers of maximum weight can, at least in principle, be approximated arbitrarily well.