Relations of APOE promoter polymorphisms to LDL cholesterol and markers of subclinical atherosclerosis in young adults

The common apolipoprotein E (apoE) gene (APOE) epsilon2/epsilon3/epsilon4 polymorphism explains part of serum lipid variation, and polymorphisms in the APOE promoter region have been proposed to participate in the regulation of serum lipid levels within the most common APOE epsilon3/epsilon3 genotype group. We determined APOE -219G/T and +113G/C promoter genotypes and estimated APOE haplotypes in 525 participants of the Cardiovascular Risk in Young Finns Study. We studied the associations of the APOE promoter polymorphisms and their haplotypes with cross-sectional and longitudinal serum lipid and apolipoprotein concentrations as well as with flow-mediated dilatation (FMD), carotid artery compliance (CAC), and intima-media thickness (IMT) within the APOE epsilon3/epsilon3 carriers. We found no significant association between the APOE promoter genotypes and serum lipids [low density lipoprotein-cholesterol (LDL-C), HDL-C, and triglycerides], apolipoproteins (apoA-I and apoB), or brachial artery FMD, CAC, or carotid IMT in either men or women. In longitudinal analyses in males, the carriers of heterozygous genotypes (-219G/T or +113G/C) and, furthermore, carriers of the -219T/+113C/epsilon3 haplotype had significantly higher LDL-C and total cholesterol concentrations throughout the 21 year follow-up period compared with homozygous G allele carriers or noncarriers of the -219T/+113C/epsilon3 haplotype. Such associations were not found in females. In summary, the APOE promoter polymorphisms -219G/T and +113G/C as well as their haplotype are associated with longitudinal changes in LDL-C and total cholesterol concentrations in young Finnish males but do not seem to be major determinants for FMD, CAC, or carotid IMT in males or females.     

Oxidative stress is decreased in off-pump versus on-pump coronary artery surgery

Oxidative stress occurs in patients undergoing coronary artery bypass operation. The aim of this study was to investigate the difference in oxidative stress in off-pump versus on-pump coronary artery bypass surgery. In the present study, in serial blood samples, plasma malondialdehyde (MDA) as index of lipid peroxidation, red blood cells glutathione peroxidase (GPx) and superoxide dismutase (SOD) were measured to compare the extent of oxidative stress in 30 patients undergoing OPCAB (off-pump coronary artery bypass grafting), 12 patients undergoing CABG (on-pump coronary artery bypass grafting) and 18 healthy controls. In CABG group, MDA levels increased significantly from 2.87 +/- 0.62 nmol/mL before anesthesia and 2.87 +/- 0.65 nmol/mL after anesthesia to 3.05 +/- 0.66 nmol/mL after ischemia (p < 0.05). Similarly, SOD levels also elevated significantly from 661.58 +/- 78.70 U/g Hb before anesthesia and 659.42 +/- 81.21 U/g Hb anesthesia induction to 678.08 +/- 75.80 U/g Hb after ischemia (p < 0.01, p < 0.01, respectively). In OPCAB group, only SOD levels increased from 581.73 +/- 86.24 U/g Hb anesthesia induction to 590.90 +/- 88.90 U/g Hb after reperfusion (p < 0.05). Glutathione peroxidase levels were not changed according to blood collection times in both of CABG group or OPCAB group (p > 0.05). Our results show that only mild signs of oxidative stress is found after reperfusion in OPCAB operation compared with CABG operation. Further studies are needed in order to confirm this hypothesis.     

Bayesian search of functionally divergent protein subgroups and their function specific residues

MOTIVATION: The rapid increase in the amount of protein sequence data has created a need for an automated identification of evolutionarily related subgroups from large datasets. The existing methods typically require a priori specification of the number of putative groups, which defines the resolution of the classification solution. RESULTS: We introduce a Bayesian model-based approach to simultaneous identification of evolutionary groups and conserved parts of the protein sequences. The model-based approach provides an intuitive and efficient way of determining the number of groups from the sequence data, in contrast to the ad hoc methods often exploited for similar purposes. Our model recognizes the areas in the sequences that are relevant for the clustering and regards other areas as noise. We have implemented the method using a fast stochastic optimization algorithm which yields a clustering associated with the estimated maximum posterior probability. The method has been shown to have high specificity and sensitivity in simulated and real clustering tasks. With real datasets the method also highlights the residues close to the active site. AVAILABILITY: Software 'kPax' is available at http://www.rni.helsinki.fi/jic/softa.html     

Multiple Displacement Amplification for Generating an Unlimited Source of DNA for Genotyping in Nonhuman Primate Species

We evaluated a whole genome amplification method—multiple displacement amplification (MDA)—as a means to conserve valuable nonhuman primate samples. We tested 148 samples from a variety of species and sample sources, including blood, tissue, cell-lines, plucked hair and noninvasively collected semen. To evaluate genotyping success and accuracy of MDA, we used routine genotyping methods, including short tandem repeat (STR) analysis, denaturing gradient gel electrophoresis (DGGE), Alu repeat analysis, direct sequencing, and nucleotide detection by tag-array minisequencing. We compared genotyping results from MDA products to genotypes generated from the original (non-MD amplified) DNA samples. All genotyping methods showed good results with the MDA products as a DNA template, and for some samples MDA improved genotyping success. We show that the MDA procedure has the potential to provide a long-lasting source of DNA for genetic studies, which would be highly valuable for the primate research field, in which genetic resources are limited and for other species in which similar sampling constraints apply.     

Human thrombin: drug stability and stabilization

Stabilization of enzymes is a key factor when using biocatalysis in practice. Each enzyme stability depends both on the structure of its molecule and on the effect of various environmental factors, thus, one of the methods of the enzyme stability preservation is the formation of optimal macromedium. Thus, water structure and enzyme hydration change in the presence of solvable additives that affects its stability and catalytic properties. The paper deals with a new method of stabilization of human thrombin developed by the authors. It is proposed to use some known organic-ligands which have ion group and different nonpolar hydrophobic groups instead of traditional additives (salts, aminoacids, polyols, polyethylene glycols etc.). Thrombin stabilization proceeds in the conditions something changed compared with traditional ones. Processes of thrombin stabilization by the above compound have been investigated, enzyme stability at different temperatures and long-term storage of diluted solutions of the preparation in different conditions have been studied. It has been established that rosselin and orange II are the most efficient ligands. Optimal finite concentrations of stabilizing agents make approximately 0.0012-0.0014 M which are rather low in the system thrombin-ligand. It has been found that diluted solutions of thrombin are more stable, than concentrated ones. In the latter case the process of autolysis is included that affects negatively the catalytic effect of the enzyme, as far as there occurs the change of thrombin molecule structure, especially of thrombin beta-chain sections, evoking conformational changes of some sites of its active centre. The experiments directed to increasing thrombin intensity in the presence of organic ligands rosselin and orange II are discussed in details. Special attention is given to autolytic method of thrombin inactivation. It is admitted on the basis of already obtained data that thrombin binding with organic ligands proceeds at the expense of anionic area of beta-domain of thrombin active centre where basic aminoacids arginin and lysine (Lys 68, Arg 78, Arg 77, Arg 66 etc.) were found. Under these conditions the hydrophobic interaction is provided at the expense of apolar binding of thrombin active centre area.     

Na+,K+-ATPase and Ca2+-ATPase isozymes in malignant neoplasms

A current state of researches on mechanisms of ion homeostasis regulation in the specific conditions of the uncontrolled malignant tumor growth (mainly in carcinomas) concerning the contribution of Na+,K+-ATPase, plasma membrane and sarco(endo)plasmic reticulum Ca2+-ATPases has been reviewed. Particular attention has been focused on the molecular and biochemical links providing the redistribution of the transporting ATPases isozyme pattern for the regulatory requirements of the cell signaling pathways at stable proliferation and viability in malignancy.     

Plasminogen activator from Agkistrodon halys halys venom

Plasminogen activator "Ahh-32" from Agkistrodon halys halys venom has been isolated and purified using affinity and ion-exchange chromatography. The purified enzyme consists of the single peptide-chain with molecular weigth of 32 kDa. It can convert free plasminogen into active form--plasmin. "Ahh-32" was inhibited by DFP and benzamidine. Besides, the enzyme influences significantly the activation of plasminogen by streptokinase without having effect on analogical process in case of usage of tissue tipe plasminogen activator. The obtained protein can be used as an instrument under investigation of protein-protein interactions in haemostasis system.     

Changed ratios of some pigments of photosynthesis in Nicotiana tabacum L. induced by exogenic DNA

The technology of obtaining the tobacco plants possessing the hereditary changes in the photosynthesis pigments accumulation during development using exogenous DNA has been elaborated. The plants possessing changes in proportion of chlorophylls content in the leave tissues, inherited elevated carotenoid content and altered proportion of carotene and xanthophylls, luteine and violaxanthine have been obtained by action of the salt-tolerant nightshade (Solanum nigrum L.) DNA and the DNAs of pCAMVNEO, pTi8628 plasmids on the tobacco cultivar Krupnolystny 20 (Large-leaf) germinating seeds. These plants have simultaneously the useful features--accelerated development, early blooming phenotype and higher productivity. Possible mechanisms emphasized such inherited biochemical changes have been discussed.