Protein sequence comparison based on the wavelet transform approach

A protein's chemical properties, the chain conformation, the function of the protein and its species specificity are determined by the information contained in the amino acid sequence. Proteins of similar functions have at some level sequential identical amino acid sequences. The closer the phylogenetic relationship, the more similar are the sequences. To find the similarities between two or more protein sequences is of great importance for protein sequence analysis. The differences in the amino acid sequences permit the construction of a family tree of evolution. In this work, a comparison method was devised that is capable of analysing a protein sequence 'hierarchically', i.e. it can examine a protein sequence at different spatial resolutions. Based on a wavelet decomposition of protein sequences and a cross-correlation study, a sequence-scale similarity concept is proposed for generating a similarity vector, which renders the comparison of two sequences feasible at different spatial resolutions (scales). This new similarity concept is an expansion of the conventional sequence similarity, which only takes into account the local pairwise amino acid match and ignores the information contained in coarser spatial resolutions.     

Auricular mild errors of morphogenesis: epidemiological study with application of a targeted computer program

Mild errors of morphogenesis (MEMs) are findings of great importance in multiple fields because of their predictive value in identification of major malformations, specific genetic syndromes, mental retardation and childhood malignancy. In order to evaluate the contribution of auricular MEMs, we constructed a computerized program, especially designed for the recording of auricular MEMs in connection with nonauricular MEMs, personal data, family, pregnancy and birth history, presence of major malformation and postural defects. The program is easy to use and delivers, at request, immediate information regarding prevalence of each auricular MEM and percentage associations between all variables. In the period from January 1, 1999 to December 31, 1999, we screened 3107 consecutively born neonates and recorded auricular and nonauricular MEMs, detected by surface examination. The general prevalence of auricular MEMs was 43.2% and the most frequent MEMs and their associates were of postural-type. This computerized program offers many advantages for the study of ear MEMs.     

Egg yolk platelet proteins from Xenopus laevis are amyloidogenic

The association of amphibian (Xenopus laevis) egg yolk platelet proteins, represented predominantly by lipovitellin, was studied as a model of the formation of amyloid deposits. Two kinds of molecular organization formed by this protein material - native and heat-denatured - were found to exhibit amyloid properties although they differ significantly in structural organization. The first consisted in protein molecules arranged in the natural, physiological, net-like platelet organization, with a tendency to orient uni-directionally. The second was obtained by the gradual removal of Congo red from lipovitellin denatured by heating in an excess of dye. This procedure produced the twisted fibrillar organization of molecules typical for amyloids, represented predominantly by end-to-end associated major polypeptide chains of lipovitellin. Both native and denatured structural forms bind Congo red and produce a green birefringence effect, confirming the near parallel alignment of the complexed Congo red molecules. However, a dye(1,4-bis(1-amino-4-sulfonaphtyl-2-azo)phenylene) closely related to Congo red but with a very weak self-assembling tendency appeared inactive when the spectral shift was studied in a cross-polarization system, indicating in this way that dye supramolecularity is an extra factor which may determine binding to amyloid proteins and specific spectral effects.     

Renal injuries induced by chronic intoxication with microcystins

The microcystins (MCs) LR and YR are hepatotoxins produced by some species of freshwater cyanobacteria. Only a few reports on the acute nephrotoxicity of MCs have been published to date. Here we investigate the effects on rat kidneys of chronic administration of relatively low doses of MC LR and MC YR. Male Wistar rats were injected every second day for 8 months with MC LR (10 microg/kg i.p., n=5) and MC YR (10 microg/kg i.p., n=5). The control group was treated with vehicle, a mixture containing 0.8 % ethanol and 0.2 % methanol in 0.9 % saline (3.7 ml/kg i.p., n=5). We found that MCs could induce damage to the kidney cortex and medulla. The lesions mainly consisted of damaged and dilated tubuli filled with homogenous eosinophil material. We conclude that long-term exposure to relatively low doses of MCs poses a considerable risk for kidney injury.     

Testing cms-P-linked AFLPs for selection of rye hybrid components

Application of AFLPs linked to pollen fertility restoration and non-performing genes evaluated in the C394-F2 hybrid was studied using a set of male sterile lines in the sterilising Pampa cytoplasm, several restorers and maintainer lines and, finally, two inbred lines backcrossed into cms-P, cms-R, cms-S and cms-C cytoplasms each. The set of male sterile lines based on the Pampa cytoplasm exhibited gradual variation in their ability to restore pollen fertility (starting from low and closing with high) in crosses with three unrelated restorers. Variations in the AFLPs between the analysed materials were observed, however, no clustering of the lines according to their sterile and fertile phenotypes was observed. The same markers, when applied to the population restorer (cv. Walet) that formed the C394-F2 cross permitted identification of plants with genotypes that could be recognized as restorers.     

Paraoxonase activity and concentration of indicators of lipids status in the serum of cardiac patients

In this research, we measured the activity of paraoxonase (basal and activated) enzyme, and components of lipid status components (total cholesterol, LDL cholesterol, HDL cholesterol and Apo A I) in the serum of patients, undergoing bypass surgery. We also tested how the applied EKC affected changes of defined indicators. Measuring of all the given parameters was conducted prior to the operation, 90 minutes, 1.5 hour, 6 hours, 24 hours and 72 hours, on 29 patients (11 of them did undergo myocardium revascularization with the application of EKC, while the rest of them did not). Activity of paraoxonase (both basal and activated) changes significantly during the postoperative period, in relation to pre-operative values, p < 0.05. Total cholesterol concentration is reduced in both examined groups, regardless of the application of EKC. This trend is also accompanied by LDL cholesterol concentration. On the other hand, HDL cholesterol concentration during post-operative period does not indicate any significant statistical change in relation to pre-operative values, while we noticed difference with regard to EKC application, 90 minutes after surgery. This change of lipid status indicator is partly due to heparin, a stimulator of lipoprotein lipase that was applied during the surgery. Our conclusion is that lipid profile changes significantly after the bypass surgery, mostly regardless of the application of EKC.     

Shear stress increases expression of a KATP channel in rat and bovine pulmonary vascular endothelial cells

We have shown previously that acute ischemia leads to depolarization of pulmonary microvascular endothelial cells that is prevented with cromakalim, suggesting the presence of ATP-sensitive K⁺ (K_ATP) channels in these cells. Thus K_ATP channel expression and activity were evaluated in rat pulmonary microvascular endothelial cells (RPMVEC) by whole cell current measurements, dot blot (mRNA), and immunoblot (protein) for the inwardly rectifying K⁺ channel (K_IR) 6.2 subunit and fluorescent ligand binding for the sulfonylurea receptor (SUR). Low-level expression of a K_ATP channel was detected in endothelial cells in routine (static) culture and led us to examine whether its expression is inducible when endothelial cells are adapted to flow. Channel expression (mRNA and both K_IR6.2 and SUR proteins) and inwardly rectified membrane current by patch clamp increased significantly when RPMVEC were adapted to flow at 10 dyn/cm² for 24 h in either a parallel plate flow chamber or an artificial capillary system. Induction of the K_ATP channel with flow adaptation was also observed in bovine pulmonary artery endothelial cells. Flow-adapted but not static RPMVEC showed cellular plasma membrane depolarization upon stop of flow that was inhibited by a K_ATP channel opener and prevented by addition of cycloheximide to the medium during the flow adaptation period. These studies indicate the induction of K_ATP channels by flow adaptation in pulmonary endothelium and that the expression and activity of this channel are essential for the endothelial cell membrane depolarization response with acute decrease in shear stress. flow adaptation; K_IR 6.2; sulfonylurea receptor; fluorescent glyburide; pulmonary microvascular endothelial cells     

Protein distorsion-derived mechanism of signal discrimination in monocytes revealed using Congo red to stain activated cells

The supramolecular dye Congo red was used to check whether monocyte activation may be mediated by a torsion-dependent mechanism preventing transduction of weak random signals in cell contacts in a way corresponding to the discrimination mechanism found in complement fixation by immune complexes. Tight cell-cell contacts generating torsional effects may be expected to produce alteration of receptor structure, making them accessible for binding of supramolecular dyes. In this study, Congo red was used to observe the binding accessibility of (1) monocytes (human) induced by contact with cancer cells (HCV29T, human), (2) monocytes (mouse) stimulated by interaction with heat-aggregated IgG and (3) monocytes (mouse) activated by rosetting in the presence of an SRBC-anti-SRBC system. Microscopic studies confirmed the activation of monocytes manifested by their clustering and Congo red binding, but only tightly clustered cells appeared to attach the dye on the surface. Usually not the whole cell surface is found to be engaged in dye complexation. Staining occurs predominantly on the interfaces of reacting cells, making probable the suggestion that cell adhesion receptors are involved in dye binding. The cells in the central areas of tight clusters undergo accelerated death. In the presence of Congo red they are easily recognized as intensely fluorescent. The characteristic localization of dead cells in the central area of clusters indicates that death is not random but results from cell activation. The role of Congo red in this process remains to be clarified. The staining characteristics of monocytes after application of Congo red probably discloses the initial step in signal transduction generated by torsional movements in receptor proteins.     

Effect of psoralens on Fenton-like reaction generating reactive oxygen species

Psoralens (psoralen, 5-methoxypsoralen, 8-methoxypsoralen, khellin, and visnagin) in 1 mM doses were shown to enhance the generation of reactive oxygen species, such as the hydroxyl radical (HO*), the superoxide anion radical (O2(-)), and singlet oxygen ((1)O(2)), from the system generating chemiluminescence (CL), as well as free radicals in the absence of light. The system that generated CL was made up of CoCl(2) and H(2)O(2). Incubation of psoralens in 0.2 mM doses with the generating system showed that only 8-methoxypsoralen and khellin have antioxidative effects. Antioxidative effects were also observed in the case of visnagin but in low concentration (0.05 mM). High doses of psoralens (1 mM) showed prooxidative effects. Measurements were done using a deoxyribose assay, the CL method, and spin-trapping with 5,5-dimethyl-1-pyrroline-N-oxide and 2,2,6,6-tetramethylpiperidine combined with electron spin resonance spectroscopy and spectrophotometry methods.     

Modulation of endothelial inward-rectifier K+ current by optical isomers of cholesterol

Membrane potential of aortic endothelial cells under resting conditions is dominated by inward-rectifier K(+) channels belonging to the Kir 2 family. Regulation of endothelial Kir by membrane cholesterol was studied in bovine aortic endothelial cells by altering the sterol composition of the cell membrane. Our results show that enriching the cells with cholesterol decreases the Kir current density, whereas depleting the cells of cholesterol increases the density of the current. The dependence of the Kir current density on the level of cellular cholesterol fits a sigmoid curve with the highest sensitivity of the Kir current at normal physiological levels of cholesterol. To investigate the mechanism of Kir regulation by cholesterol, endogenous cholesterol was substituted by its optical isomer, epicholesterol. Substitution of approximately 50% of cholesterol by epicholesterol results in an early and significant increase in the Kir current density. Furthermore, substitution of cholesterol by epicholesterol has a stronger facilitative effect on the current than cholesterol depletion. Neither single channel properties nor membrane capacitance were significantly affected by the changes in the membrane sterol composition. These results suggest that 1) cholesterol modulates cellular K(+) conductance by changing the number of the active channels and 2) that specific cholesterol-protein interactions are critical for the regulation of endothelial Kir.