Deoxyribozyme-based ligase logic gates and their initial circuits

A complete set (YES, NOT, AND, and ANDNOT) of molecular scale logic gates based on ligase deoxyribozymes was constructed. The activity of these gates was visualized through the formation of cascades with downstream phosphodieseterase YES gates, which performed fluorogenic cleavage.     

Electrophoretic analysis of oxidatively modified eye lens proteins in vitro: implications for diabetic cataract

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles of eye lens proteins showed that both progression of diabetic cataract in rats in vivo and precipitation of soluble eye lens proteins stressed by free radicals in vitro were accompanied by significant protein cross-linking. There was a noticeable contribution of disulfide bridges to protein cross-linking in diabetic eye lens in vivo. In contrast, under conditions in vitro, when eye lens proteins were exposed to hydroxyl or peroxyl radicals, we showed that the participation of reducible disulfide linkages in the formation of high molecular mass products was markedly lower. These in vivo--in vitro differences indicate that the generally accepted role of reactive oxygen species in diabetic cataractogenesis may be overestimated in connection with the processes of protein cross-linking.     

New intra-intermolecular criss-cross cycloaddition of unsymmetrical allenylazines with alkynes leading to three fused five-membered heterocycles

This report describes a new type of intra-intermolecular criss-cross cycloadditions. Thermal reactions of unsymmetrical allenylazines in the presence of alkynes led to three fused five-membered heterocycles in some cases. In the case of unsymmetrical substituted alkynes, a regioselectivity was observed. The molecular structures of all products are discussed. One X-ray crystal structure is also reported.     

Mathematical modeling of the relation between myosin phosphorylation and stress development in smooth muscles

In this paper the 4-state latch bridge model proposed by Rembold and Murphy is expanded; first by incorporation of the analytical expression of Ca2+ dependent MLCK activation from the work of Kato et al. and second, by inclusion of the myosin dephosphorylation based on the Michaelis-Menten kinetics. The analysis of the proposed model and the comparison with the original model results as well as with the experimental data is presented. The model is able to predict the steady-state isometric stress and the myosin phosphorylation in dependence on steady cytosolic [Ca2+] as well as the temporal evolution of the system in dependence on the input Ca2+ signal in the form of biphasic transient, whereby our model results are in several aspects in better agreement with experimental observations.     

Novel characterization of proteomics maps by sequential neighborhoods of protein spots

We consider a characterization of proteomics maps based on an alternative kind of neighborhood graphs for the protein spots on 2-D gel. The novel approach considers for every protein spot only the nearest neighborhood consisting of protein spots of higher abundance. The approach has the simplicity and advantages of the recently introduced characterization of proteome maps based on considering the nearest neighborhoods of protein spots, but it also has important additional desirable computational features. The characterization of the nearest neighborhood graphs of 2-D gel proteomics maps is sensitive to the number of spots considered and may lead to changes in the degree of similarity of different maps when the number of points has been changed, thus imposing restrictions on the protocol used for comparison of maps. The novel approach presented in this work is less sensitive to the number of points used in the analysis because graphs are constructed in a stepwise process in which the role of more distant neighbors has been diminished by linking a new spot to the nearest spot that has been already part of the neighborhood graph. In this way a graph with N + 1 spots is obtained from the graph on N spots by adding a single new link, while in the case of the nearest neighborhood graphs adding a new spot introduces novel neighborhoods and generally results in a graph that may differ significantly from the neighborhood graph on N points.     

On‐line flow‐through extraction–preconcentration‐large volume injection‐RP LC for trace determination of pyrethroids in Slovak soil

A rapid micro‐analytical multiresidue method was developed for analysis of pyrethroids (kadethrin K, cypermethrin C and permethrin P) in soil micro‐sample (200 mg). It uses on‐line flow‐through extraction of soil micro‐samples (packed into a short glass column) with a methanol‐aqueous citric acid buffer mixture, successive on‐line SPE preconcentration of analytes from the extract and on‐line RP‐HPLC analysis with UV photometric detection. The separation of pyrethroids is performed on a Purospher RP‐18e column with methanol/water as mobile phase. Effects of sorbent placed at the bottom of a short column holding the soil sample and different kinds of on‐line SPE columns were tested. Besides, the influence of volume of the effluent on the pyrethroids recovery was also studied. Calibration curves were linear over the range assayed from 0.01 to 0.2 μg/mL with correlation coefficients of linear regression (least‐squares method) in the range 0.998–0.999. Recovery studies were carried out at 0.25–1.00 μg/g dry soil fortification level and obtained recoveries were for K 81–84%, C 56–59% and for P 58–63%. Achieved LOD (confidence band) of studied pyrethroids were for large‐volume injection (1 mL) 4.5 ng K, 3.7 ng C, 3.6 ng P or 27 ng/g K, 32 ng/g C and 29 ng/g P in dry soil “solid sampling HPLC”.     

HPLC analysis of a syrup containing nimesulide and its hydrolytic degradation product

The present paper deals with the evaluation of nimesulide, 2-phenoxy-4-nitroaniline, the main hydrolytic degradation product of nimesulide, of methylparaben and propylparaben, and eventually of 4-hydroxybenzoic acid by HPLC with UV detection at 254 nm in syrup as a pharmaceutical formulation. HPLC analysis was employed on the reversed phase C18 with methanol and 0.01 M dibasic ammonium phosphate (ρ _r = 60: 40, pH 4.0). Validation was performed using standards and a pharmaceutical preparation containing the compounds described above.     

[Cu(X-salicylato)2(N,N-diethylnicotinamide)2(H2O)2] complexes: conformational polymorphism and its consequence in supramolecular hydrogen-bonding networks formation

Novel copper(II) X-salicylate complexes with N,N-diethylnicotinamide (dena) of the formula [Cu(RCOO)₂(dena)₂(H₂O)₂] (RCOO = 3-methylsalicylate anion (3-Mesal, 1), 4-methylsalicylate anion (4-Mesal, 2), 5-methylsalicylate anion (5-Mesal, 3), 5-methoxysalicylate anion (5-MeOsal, 4) or 4-methoxysalicylate anion (4-MeOsal, 5)), and complex [Cu(3-MeOsal)₂(dena)₂(H₂O)₂]∙2H₂O (3-MeOsal = 3-methoxysalicylate anion (6)) have been prepared in the crystalline forms and characterized by spectroscopic methods (IR, Vis–UV, EPR). All the compounds according to their composition (1–5) seem to possess octahedral copper(II) stereochemistry. The complex 1 has been prepared in two different forms. X-ray analyses of the complexes 1, 4, and 5 were carried out and they featured a tetragonal-bipyramidal geometry around the copper atoms. The tetragonal planes are created by X-salicylate anions bonded to the copper(II) atoms via unidentate carboxylate oxygen atoms and the pyridine ring nitrogen atoms of the neutral ligand N,N-diethylnicotinamide, while in axial positions are water molecules. The two forms of complex 1 present conformation polymorphs and supramolecular isomers.     

Gas phase and solution state stability of complexes L…M, where M = Cu, Ni, or Zn and L = R−C(O)NHOH (R = H, NH2, CH3, CF3, or Phenyl)

The structure and gas-phase metal affinities (M = Cu²⁺, Ni²⁺, and Zn²⁺) of formohydroxamic acid derivatives R–C(O)NHOH (R = H, NH₂, CH₃, CF₃ and Phenyl) were studied using the B3LYP/6-311+G(d,p) method of DFT theory. In order to evaluate the conformational behavior of these systems in water, we carried out CPCM-SCRF optimization calculations at the B3LYP/6-311+G(d,p) levels of theory. The obtained optimized geometries and interaction affinities of the gas and solution phase were compared. The following order of stability was found for ionic complexes of the transition metals: Cu²⁺ > Ni(t)²⁺ > Zn²⁺. The same stability order would be expected according to the Irving–Williams order of stability constants. The high-spin complexes of the Ni²⁺ were more stable than the low-spin complexes. The solvent effect reduced the observed relative stability of individual metallic complexes of substituted hydroxamic acids.