How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?

To estimate how sophisticated should an empirical scoring function be to ensure successful docking, scoring and virtual screening a new scoring function NScore (naive score) has been developed and tested. NScore is an extremely simple function and has the minimum possible number of parameters; nevertheless, it allows all the main effects determining the ligand–protein interaction to be taken into account. The fundamental difference of NScore from the currently used empirical functions is that all its parameters are selected on the basis of general physical considerations, without any adjustment or training with the use of experimental data on ligand–protein interaction. The results of docking and scoring with the use of NScore in an independent test sets of proteins and ligands have proved to be as good as those yielded by the ICM, GOLD, and Glide software packages, which use sophisticated empirical scoring functions. With respect to some parameters, the results of docking with the use of NScore are even better than those obtained using other functions. Since no training set is used in the development of NScore, this scoring function is indeed versatile in that it does not depend on the specific goal or target. We have performed virtual screening for ten targets and obtained results almost as good as those yielded by the Glide and better than GOLD and DOCK software. Figure Average percent of known actives found vs percent of the ranked database screened (x axis) for NScore (NScore, black)- an extremely simple function where all parameters are selected on the basis of general physical considerations, without any adjustment or training with the use of experimental data, Glide XP (XP, red), Glide SP (SP, green), DOCK (DOCK, blue), GOLD GoldScore1x (gold1x, cyan), and GOLD ChemScore1x (chem1x, magenta). Grey lines (rand show results expected by chance.     

Chromosome numbers in Brazilian species of Crotalaria (Leguminosae, Papilionoideae) and their taxonomic significance

Chromosome numbers were counted for 23 species of Crotalaria native to Brazil. Among these data there were new counts for 15 taxa, and some confirmed previous reports or represented numbers that were different from those cited previously. The chromosome numbers most frequently found were 2 n  = 16 and 2 n  = 32. Only C. incana L. had 2 n  = 14 and C. tweediana Benth. had 2 n  = 54. The counts 2 n  = 32 and 54 were found in species of section Calycinae and 2 n  = 16 and 14 in species of section Chrysocalycinae . The data revealed the importance of chromosomal parameters in the characterization of sections Calycinae and Chrysocalycinae in Brazil. We discuss the systematic significance and evolutionary aspects for the genus, comparing the results with the two sections that are native in Brazil.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 271–277.     

Importance of DNA methylation in the inheritance of radiation-induced aberrant expression of microRNA

We studied microRNA gene expression in HeLa cells following exposure for 6 h and 8 days to Co⁶⁰ gamma rays at a dose of 4 Gy using an approach of large-scale parallel DNA sequencing. We identified 12 microRNAs with aberrant expression which were maintained in cell generations. The analysis of radiation-induced aberrant expression of pre-microRNAs made it possible to assess the importance of nuclear and cytoplasmic stages of microRNA biogenesis for preservation of its aberrant expression. On cell treatment by 5-azacytidine, aberrant expression was maintained only in two microRNAs: miR-21-3p and miR-422a, which demonstrated an increase in expression. Radiation-induced decrease in expression in ten examined microRNAs was dependent on DNA demethylation. At the same time, expression in a microRNA set, which demonstrated inheritable alteration of the expression after gamma-radiation exposure in the untreated cells, was not dependent or was weakly dependent on DNA methylation. The obtained results suggest that ionizing radiation induces aberrant DNA methylation, which affects inherited expression changes in microRNAs in cell generations after exposure to the mutagen.     

Chromosome numbers and meiotic analysis in the pre-breeding of <Emphasis Type="BoldItalic">Brachiaria decumbens</Emphasis> (Poaceae)

A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented 2n = 18; 27 accessions, 2n = 36; and 2 accessions, 2n = 45 chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.     

Two immunologically distinct types of protofilaments can be identified in Natrialba magadii flagella

A rabbit antiserum to the 15-kDa acetylcholinesterase toxin neutralised the lethal effect of the 15-kDa toxin of Aeromonas hydrophila when injected into trout. However, immunisation of fish with the 15-kDa toxoid failed to induce an antibody response, and a higher molecular mass form of this toxin was purified from the extracellular products with the aim of inducing an immune response in fish. The optimal conditions for production of extracellular products by A. hydrophila strain B32 were studied to increase the concentration of this protoxin. The extracellular products were fractionated by molecular exclusion chromatography to yield a purified protoxin with an estimated molecular mass of 45 kDa by SDS-PAGE and which gave a positive reaction in Western blotting with the rabbit anti-15-kDa toxin serum. Since the 45-kDa protoxin showed lower specific acetylcholinesterase activity than the active 15-kDa toxin, the behaviour of the active site was studied using specific inhibitors. This 45-kDa protoxin was 13.3-fold less toxic than the 15-kDa toxin and induced antibody production in fish.     

Hormone-dependent insertional Arabidopsis thaliana mutants with decreased viability and fertility

We present data on the phenotype identification and genetic analysis of offspring in three lines of dominant morphological mutants of Arabidopsis thaliana having drastically reduced fertility (a sterile calluslike mutant, a flower mutant, and a dwarf mutant) and in five lines of recessive morphological mutants (four mutants with lethal seedlings and one pigmentation mutant). The mutants were selected from a collection of transgenic plants that had genomes carrying a T-DNA insertion of plasmid vectors pLD3 and pPCVRN4; the collection was created earlier via agrobacterial transformation of germinating seeds. The results presented here were obtained using compensation of hormonal imbalance in the insertional morphological mutants of A. thaliana by exogenous hormones.     

Isolation and characteristics of compound transposons Tn1000::Tn5

Two types of compound transposons were derived. In the first case, transposon Tn5 is inserted into the gene responsible for Tn1000 transposase synthesis. In the other, Tn5 is inserted into the region near the left end of Tn1000, where no functionally significant genes were found. It is known that translocation of the compound transposons does not depend on their size and takes place with the efficiency close to that characteristic of the intact Tn1000. Insertion of Tn5 into the gene coding for Tn1000 transposase results in sharp decrease in the efficiency of Tn1000 translocations. This effect, however, may be eliminated by introduction into the cell of the intact Tn1000.     

The study of structure-antiarrhythmic activity relationship of N-phenylacetamide derivatives and aromatic carbonic acid amides

Using the SARD-21 (Structure Activity Relationship & Design) computer system, structural features of high- and low-effective antiarrhythmic agents have been recognized and the influence of these features on the antiarrhythmic properties has been evaluated. This information has been used for generation of the model to predict antiarrhythmic effectiveness of pharmaceutical preparations at the recognition level of 82% by means of two different approaches. The recognized structural parameters may be successfully used to design new highly effective antiarrhythmic drugs, and also to modify structures of the already-existing anti-arrhythmic drugs in order to increase the effectiveness of their antiarrhythmic action.     

Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans

The genetic variability at six cloned minisatellite loci was analyzed in minke whale populations from the North Atlantic, North Pacific, and Antarctic Oceans. Three loci displayed only a few different alleles in each of the three populations, with heterozygosity ranging from 0.00 to 0.47, and three loci revealed many different alleles in at least two fo the three populations, with heterozygosity ranging up to 0.98. Using small sample sizes, samples from two adjacent Antarctic Management Areas were not found to differ significantly in allele frequencies at any of the six loci. The use of principal coordinate analysis to detect multilocus disequilibria was explored. No significant evidence was found of intrapopulation heterogeneity within the pooled Antarctic sample. Pronounced interoceanic differences were observed at every locus, confirming the existence of genetic isolation found earlier using more conventional marker systems. The populations from the three oceans appear to have diverged to such a degree that the hypervariable loci have had time to evolve independently and arrive at different evolutionary stages in different populations. The frequency of undetected "null" alleles is remarkably high in minke whale populations compared to human populations and is probably a result of the cloning protocol used. Minisatellite loci are shown to provide a powerful population genetic tool, supplying levels of resolution appropriate to different degrees of evolutionary divergence.