Antibiotic sensitivity of bacteria isolated in 1998 and 1999 from patients with infections of upper airways residing in Western Pomerania.

Sensitivity to antibiotics of the most common pathogens isolated from the upper airways in north-west part of Poland shown significant regional variation. The rise in resistance to penicillin for Streptococcus pneumoniae (to 22%) and to macrolides for Streptococcus pyogenes, Streptococcus pneumoniae and Staphylococcus aureus was observed. No differences in sensitivity have been found between pathogens isolated from hospital and ambulatory patients.

[Biocompatibility assessment of aqueous extracts from new multiblock poly(ester-ester) copolymer]. / Badania biologiczne wyciagów wodnych z nowego multiblokowego poli(estro-estro) kopolimeru.

In the Technical University of Szczecin, Department of Chemical Fibres and Physical Chemistry of Polymer there has been synthesised a new polymer based on butylene terephthalate--PBT and dimerized fatty acid--DFA. Five different polymers varying in mechanical properties depending on hard segments--PBT and soft segments--DFA composition were obtained. Assessment of biocompatibility of the new materials was conducted according to FDP. Prepared water extracts from polymers were applicated intravenously to mouse and intra-abdominaly to mice and guinea pigs. All animals survived spell of the experiment and no signs of physical degradation were noticed. Kidney, liver, spleen, heart and peritoneum specimens was taken and evaluated microscopically. There was no signs of toxic action of the extracts. Based on principles in FDP and the data from animal studies it is applicable that evaluated materials have no increased toxicity.

DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer.

DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller*.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the *.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).

Geometries and energies of Watson-Crick base pairs in oligonucleotide crystal structures.

We analyzed geometries and energies of 469 GC and 224 AT pairs occurring in 11 A-, 54 B- and 12 Z-DNA crystal structures. The most frequent hydrogen bond length conforms to the canonical value but distributions of the hydrogen bond lengths are unexpectedly wide. The average GC pair is rather compressed and opened into the double helix minor groove while an average AT pair has canonical dimensions. The extreme base pair geometrical parameters are the following: buckle -26 degrees and 39 degrees, propeller -33 degrees and 26 degrees, opening -23 degrees and 19 degrees, shear -1.4 A and 2.1 A, stretch -0.7 A and 0.4 A, and stagger -2.3 A and 1.8 A. The analyzed set contains complementary bases apparently bound by unusual bifurcated hydrogen bonds. The unusual base pairing geometries are of two kinds. In the first case, an extreme value of one parameter is compensated for by other geometrical parameters so that the energy of the resulting geometry is acceptable. However, there are also examples when the compensatory effect is missing and then the base pairing instability is dramatic. The most extensive base pair deformations occur in dodecamers, the d(GGATGGGAG) nonamer, the r(UUAUAUAUAUAUAA) 14-mer, and the d(ICCGG) tetramer whose common feature is a low structure resolution. However, very unstable base pairs are also present in the decamer d(CCAACGTTGG) and hexamer d(CGTACG) whose structures were solved at a relatively high resolution. As the deformations probably originate from crystal packing forces and/or data and refinement errors, we recommend to omit these structures from studies of DNA sequence-structure relationships. The remaining hexamers, octamers and decamers whose list and their Watson-Crick base pair characteristics are given in the article are suitable for this purpose because they exhibit no prohibitive energy deviations from the canonical hydrogen bonding properties.

Propeller-twisted adenine.thymine and guanine.cytosine base pairs tend to buckle and stagger in opposite directions.

Base pairs are propeller-twisted, buckled and staggered in DNA fragment crystals. These deformations were analyzed with isolated Watson-Crick base pairs using empirical potentials and buckle was found to almost linearly correlate with propeller. Interestingly, the thymine.adenine pair favours negative buckling for propellers mostly observed in DNA crystals while positive buckling is preferred by the cytosine.guanine pair. The propeller also induces opposite staggers in the adenine.thymine and guanine.cytosine base pairs.

Mutual backbone phosphate group interactions promote DNA double helix bending at high salt concentrations in solution.

Results of free energy calculations connected with the backbone phosphate group interactions upon local bending and helical twist modifications of A-, B- or Z-DNA at high salt concentrations have been reported recently (Jursa and Kypr 1990). Here we calculate energies necessary for DNA bending, using three models based on experimentally determined persistence length values. A comparison of energies following from the two quite different approaches suggests that high salt concentrations induce A- and mainly B-DNA bending into the double helix minor groove at least up to 10 degrees.

Mutual interactions of the phosphate groups in locally deformed backbones of various DNA double helices at high salt concentrations.

Changes in the free energy of mutual phosphate group interactions are calculated that accompany bending of the A-, B- and Z-DNA backbones in 0.7, 2.1 and 4.2 mol/l NaCl aqueous solutions. The bending is often found to be favoured in the direction of the double helix grooves; B-DNA prefers bending into the major groove while minor groove is the preferred bending direction of A-DNA in the presence of 0.7 mol/l NaCl. Interestingly, the preferences are reversed in 4.2 mol/l NaCl. Further stabilization of A-DNA and B-DNA backbones is achieved in some cases if bending is combined with suitable local double helix twist alterations. Bending tendencies of Z-DNA backbone are generally weaker and they decrease, in contrast to B-DNA and A-DNA, with the increasing ionic strength.