Substituted p-hydroquinones as inhibitors of lipid peroxidation

The technique based on monitoring oxygen consumption was applied to study 12 alkyl- and methoxy-substituted p-hydroquinones (QH(2)) as a chain-breaking antioxidant during the oxidation of styrene and methyl linoleate (ML) in bulk as well as ML oxidation in micellar solution of sodium dodecyl sulfate (SDS) at 37 degrees C. The antioxidant activities of QH(2) were characterized by two parameters: the rate constant k(1) for reaction of QH(2) with the peroxy radical LO(2)*: QH(2)+LO(2)*-->QH*+LOOH and the stoichiometric factor of inhibition, f, which shows how many kinetic chains may be terminated by one molecule of QH(2). In the case of styrene and ML oxidation in bulk, f values never exceed two; for the majority of QH(2), f was found to be significantly less than two due to the interaction of QH* with molecular oxygen. In the absence of superoxide dismutase (SOD), all the studied QH(2) displayed a very moderate if any antioxidant capability during ML oxidation in SDS micelles. When 20U/ml SOD was added, the majority of QH(2) showed a pronounced ability to inhibit ML oxidation, f parameter being ca. one. The features of QH(2) as an antioxidant in aqueous environment are suggested to associate with the reactivity of semiquinone (Q*(-)). Q*(-) reacts readily with molecular oxygen with formation of superoxide (O(2)*(-)); further reactions of O(2)*(-) result in fast depleting QH(2) and chain propagation. The addition of SOD results in purging a reaction mixture from O(2)*(-) and, as a corollary, in depressing undesirable reactions with the participation of O(2)*(-). With all the oxidation models, QH(2) were found to be very reactive to LO(2)*. The rate constants k(1) decreased progressively when going from the oxidation of styrene to ML oxidation in bulk and further to ML oxidation in SDS micelles.     

The first evidence of anaerobic CO oxidation coupled with H<Subscript>2</Subscript> production by a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent

From 24 samples of hydrothermal venting structures collected at the East Pacific Rise (13°N), 13 enrichments of coccoid cells were obtained which grew on CO, producing H₂ and CO₂ at 80°C. A hyperthermophilic archaeon capable of lithotrophic growth on CO coupled with equimolar production of H₂ was isolated. Based on its 16S rRNA sequence analysis, this organism was affiliated with the genus Thermococcus. Other strains of Thermococcales species (Pyrococcus furiosus, Thermococcus peptonophilus, T. profundus, T. chitonophagus, T. stetteri, T. gorgonarius, T. litoralis, and T. pacificus) were shown to be unable to grow on CO. Searches in sequence databases failed to reveal deposited sequences of genes related to CO metabolism in Thermococcales. Our work provides the first evidence of anaerobic CO oxidation coupled with H₂ production performed by an archaeon as well as the first documented case of lithotrophic growth of a Thermococcales representative.     

Seven clusters in genomic triplet distributions

In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring a learning dataset of already known genes. The fact that unsupervised gene-detection is possible is closely connected to the existence of a cluster structure in oligomer frequency distributions. In this paper we study the cluster structure of several genomes in the space of their triplet frequencies, using a pure data exploration strategy. Several complete genomic sequences were analyzed, using the visualization of tables of triplet frequencies in a sliding window. The distribution of 64-dimensional vectors of triplet frequencies displays a well-detectable cluster structure. The structure was found to consist of seven clusters, corresponding to protein-coding information in three possible phases in one of the two complementary strands and in the non-coding regions with high accuracy (higher than 90% on nucleotide level). Visualizing and understanding the structure allows to analyze effectively the performance of different gene-prediction tools. Since the method does not require extraction of ORFs, it can be applied even for unassembled genomes.     

Phosphorodiamides as prodrugs for antiviral nucleosides

New phosphorodiamides of modified nucleoside monophosphates were synthesized and their antiviral properties were evaluated.     

The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold

Holliday junction resolution performed by a variety of structure-specific endonucleases is a key step in DNA recombination and repair. It is believed that all resolvases carry out their reaction chemistries in a similar fashion, utilizing a divalent cation to facilitate the hydrolysis of the phosphodiester backbone of the DNA, but their architecture varies. To date, with the exception of bacteriophage T4 endonuclease VII, each of the known resolvase enzyme structures has been categorized into one of two families: the integrases and the nucleases. We have now determined the structure of the Escherichia coli RusA Holliday junction resolvase, which reveals a fourth structural class for these enzymes. The structure suggests that dimer formation is essential for Mg(2+) cation binding and hence catalysis and that like the other resolvases, RusA distorts its Holliday junction target upon binding. Key residues identified by mutagenesis experiments are well positioned to interact with the DNA.     

Design and synthesis of pseudo-symmetric HIV protease inhibitors containing a novel hydroxymethylcarbonyl (HMC)-hydrazide isostere

Pseudo-symmetric HIV-1 protease inhibitors containing a novel HMC-hydrazide isostere as the transition-state mimic were designed and synthesized. Most of the synthetic compounds with varied structures at the P and P' sites around this core unit showed potent inhibitory activity against HIV-1 protease with nanomolar K(i) values.     

P-selectin blocking potency of multimeric tyrosine sulfates in vitro and in vivo

P-selectin blocking potency was investigated using synthetic monomeric and polymeric anionic compounds containing sulfate groups such as O-sulfotyrosine (sTyr) and/or sulfated Lewis structures. A non-carbohydrate-containing polyacrylamide conjugate sTyr-PAA (80% mol of sTyr) was a remarkably potent inhibitor of P-selectin binding in vitro, having an IC(50) value of 6 ng/mL (equivalent to 10 nM calculated on the basis of sTyr residues or 0.1 nM calculated by the mass of the macromolecule). The inhibitory effect of sTyr-PAA (80%) towards P-selectin is significantly greater than that of fucoidan (IC(50), 100 ng/mL). However, sTyr-PAA (80%) was less effective than fucoidan at reducing neutrophil extravasation in an in vivo rat model of peritonitis.     

Zinc causes loss of membrane potential and elevates reactive oxygen species in rat brain mitochondria

Emerging evidence suggests that Zn2+ may impair neuronal metabolism. We examined how Zn2+ affects the activity of isolated brain mitochondria fueled with glutamate + malate, succinate or glycerol 3-phosphate. Submicromolar levels of Zn2+ dissipated membrane potential and inhibited oxygen utilization in all three substrate conditions. Zn(2+)-induced depolarization was reversed by the membrane-impermeant metal chelator, EGTA, and was inhibited by uniporter blockade. Cyclosporin A did not block Zn(2+)-induced depolarization. Added Zn2+ increased accumulation of reactive oxygen species (ROS) in glutamate + malate or glycerol 3-phosphate conditions, but inhibited succinate-supported ROS accumulation. These results show that Zn2+ blocks mitochondrial function in all physiologically relevant substrate conditions.     

Bone mineralization and physical development of children

A cross-sectional study of BMD and physical development values in children of various age-specific groups was carried out. In all, the study included 357 children (194 boys and 163 girls) aged from 5 to 16 years. The study did not include children with inherited or acquired diseases of the musculoskeletal system, chronic diseases of the liver or kidneys, diabetes, thyrotoxicosis or malabsorption syndrome or professional athletes. BMD values were estimated by dual X-ray absorbtiometry (DXA) of the lumbar part of the spine (L2-L4) using a "DPX-MD+" device equipped with a "child" software program. Out of all the examined children, 58.9% had harmonic physical development, and 13.1% had a decreased body height and body mass. It was revealed that BMC and BMD values in the lumbar part of the spine intensively increased with age. BMC closely correlates with body height (r = 0.8; p < 0.000) and body mass (r = 0.7; p < 0.000). BMD also correlates with anthropometric parameters. The lowest BMC and BMD values and Z-score as well can be found in children with a low body height and body mass (<10th percentile).     

Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences

Coding information is the main source of heterogeneity (non-randomness) in the sequences of microbial genomes. The heterogeneity corresponds to a cluster structure in triplet distributions of relatively short genomic fragments (200-400 bp). We found a universal 7-cluster structure in microbial genomic sequences and explained its properties. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy. Based on the analysis of 143 completely sequenced bacterial genomes available in Genbank in August 2004, we show that there are four "pure" types of the 7-cluster structure observed. All 143 cluster animated 3D-scatters are collected in a database which is made available on our web-site (http://www.ihes.fr/~zinovyev/7clusters). The findings can be readily introduced into software for gene prediction, sequence alignment or microbial genomes classification.