Analysis of similarity of electrophoretic patterns in mRNA differential display

We present a novel method of statistical analysis for the comparison of electrophoretic data. The method is based on the squared Euclidian distance of normalized signal data vectors of electrophoretic lanes. The differences in the electrophoretic patterns are evaluated by a statistical test based on Hubert's statistics which measures the significance of the signal grouping. We demonstrate the validity and applicability of the method in a large data set derived from automated fluorescent mRNA differential display analysis of the expression of acute-phase proteins during experimental Escherichia coli infection in mice. The current testing method is capable of finding theoretically similar natural groupings to be similar in a statistically significant way whereas theoretically dissimilar or random groupings can be recognized to be artifactual. We also show how the calculated pairwise signal distances can be utilized in methodological problem solving. These analytical methods can be applied to the study of other related problems of similarity analysis of electrophoretic patterns, and also provide useful tools for the development of automated recognition of differentially expressed mRNAs.     

Three polymorphs of 4‐4′‐diiodobenzalazine,and 4‐chloro‐4′‐iodobenzalazine

Three polymorphs of 4,4′‐diiodobenzalazine (systematic name: 4‐iodobenzaldehyde azine), C₁₄H₁₀I₂N₂, have crystallographically imposed inversion symmetry. 4‐Chloro‐4′‐iodobenzalazine [systematic name: 1‐(4‐chlorobenzylidene)‐2‐(4‐iodobenzylidene)diazane], C₁₄H₁₀ClIN₂, has a partially disordered pseudocentrosymmetric packing and is not isostructural with any of the polymorphs of 4,4′‐diiodobenzalazine. All structures pack utilizing halogen–halogen interactions; some also have weak π (benzene ring) interactions. A comparison with previously published methylphenylketalazines (which differ by substitution of methyl for H at the azine C atoms) shows a fundamentally different geometry for these two classes, namely planar for the alazines and twisted for the ketalazines. Density functional theory calculations confirm that the difference is fundamental and not an artifact of packing forces.     

Isomeric Schiff bases related by dual imino‐group reversals

Two isomeric pairs of Schiff bases, N,N′‐bis­(2‐methoxy­benzyl­idene)‐p‐phenyl­enediamine, C₂₂H₂₀N₂O₂, (I), and 2,2′‐dimeth­oxy‐N,N‐(p‐phenyl­enedimethyl­ene)dianiline, C₂₂H₂₀N₂O₂, (II), and (E,E)‐1,4‐bis­(3‐iodo­phen­yl)‐2,3‐diaza­buta‐1,3‐diene (alternative name: 3‐iodo­benzaldehyde azine), C₁₄H₁₀I₂N₂, (III), and N,N′‐bis­(3‐iodo­phen­yl)ethylenedi­imine, C₁₄H₁₀I₂N₂ [JAYFEV; Cho, Moore & Wilson (2005). Acta Cryst. E 61 , o3773–o3774], differ pairwise only in the orientation of their imino linkages and in all four individual cases occupy inversion centers in the crystal, yet all four compounds are found to assume unique packing arrangements. Compounds (I) and (II) differ substantially in mol­ecular conformation, possessing angles between their ring planes of 12.10 (15) and 46.29 (9)°, respectively. Compound (III) and JAYFEV are similar to each other in conformation, with angles between their imino linkages and benzene rings of 11.57 (15) and 7.4 (3)°, respectively. The crystal structures are distinguished from each other by different packing motifs involving the functional groups. Inter­molecular contacts between meth­oxy groups define an R₂²(6) motif in (I) but a C(3) motif in (II). Inter­molecular contacts are of the I⋯I type in (III), but they are of the N⋯I type in JAYFEV.     

Redox- and protonation-state driven substrate-protein dynamics in respiratory complex I

Respiratory complex I is a key enzyme in the electron transport chains of mitochondria and bacteria. It transfers two electrons to quinone and couples this redox reaction to proton pumping to electrically charge the membrane it is embedded in. The charge and pH gradient across the membrane drives the synthesis of ATP. The redox reaction and proton pumping in complex I are separated in space and time, which raises the question of how the two reactions are coupled so efficiently. Here, we focus on the unique ～35 Å long tunnel of complex I, which houses the binding site of quinone reduction. We discuss the redox and protonation reactions that occur in this tunnel and how they influence the dynamics of protein and substrate. On the basis of recent structural data and results from molecular simulations, we review how quinone reduction and dynamics may be coupled to proton pumping in complex I.     

Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis

Journal of Computer-Aided Molecular Design - Enterococcus faecalis, a gram-positive bacterium, is among the most common nosocomial pathogens due to its limited susceptibility to antibiotics and its...     

Assessment of labelled products with different radioanalytical methods: study on 18F-fluorination reaction of 4-[18F]fluoro-N-[2-[1-(2-methoxyphenyl)-1-piperazinyl]ethyl-N-2-pyridinyl-benzamide (p-[18F]MPPF)

The serotonin receptor 5-HT_1A ligand 4-[¹⁸F]fluoro-N-[2-[1-(2-methoxyphenyl)-1-piperazinyl]ethyl-N-2-pyridinyl-benzamide (p-[¹⁸F]MPPF) was produced by a simplified method of Le Bars et al. Traditional oil bath heating was compared to microwave heating. Various radioanalytical methods, radio-Thin Layer Chromatography (TLC), High Pressure Liquid Chromatography (HPLC) and Mass Spectrometry (MS), were compared in the evaluation of the labelled product(s). The crude reaction mixture consisted of p-[¹⁸F]MPPF and 2–4 radioactive by-products eluting after the product fraction, and the reverse-phase HPLC method failed occasionally to separate p-[¹⁸F]MPPF from the radioactive by-product with close retention time. The heating method had no significant effect on the composition of labelled by-products. In LC-(ESI)-MS analysis of p-[¹⁸F]MPPF the labelled product was identified with m/z ratio of 435 ([M + H⁺]). The other HPLC fractions were measured to have following m/z ratios: (1) 327; 349; (675) (2) 402; 407/408; (791) and (3) 436, suggesting different kind of decomposition of the labelled product and/or the inactive precursor. The ion trap mass spectrometer was sufficient for the qualitative analysis of p-[¹⁸F]MPPF. However, differentiation of by-products arising from the decomposition of p-[¹⁸F]MPPF or from its precursor p-MPPNO₂ proved to be challenging.