An extension of the dehoff growth path analysis

Growth path analysis is discussed from both deterministic and stochastic points of view. If nucleation is assumed deterministic, the number density function is a solution of the continuity equation. If nucleation is considered a stochastic process, the number density function loses its meaning and must be replaced by a probability density function. Im portant implications of stochastic nucleation are discussed.     

An extension of the dehoff growth path analysis

Growth path analysis is discussed from both deterministic and stochastic points of view. If nucleation is assumed deterministic, the number density function is a solution of the continuity equation. If nucleation is considered a stochastic process, the number density function loses its meaning and must be replaced by a probability density function. Im portant implications of stochastic nucleation are discussed.     

Genotyping HIV-1 and HCV strains by a combinatorial DNA melting assay (COMA)

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) strains can be genetically classified into genetic lineages known as genetic types or subtypes according to phylogenetic analyses of complete or partial nucleotide sequences of their genomes. The genetic classification of HIV-1 and HCV strains has important implications for the development of globally effective vaccines and for the management of patients. MATERIALS AND METHODS: A new method, termed combinatorial DNA melting assay (COMA), allows rapid accessing of comparative genetic information between related DNA sequences, making it possible to rapidly and accurately genotype unknown HIV-1 and HCV strains. COMA is mainly based on the differential melting properties of long DNA heteroduplexes. Combinatorial arrays of DNA heteroduplexes are formed when captured PCR-amplified reference DNA with known nucleotide sequences are combined with solution-phase complementary and antigenically labeled DNA with unknown sequences. Genetic divergence between the known and the unknown sequences is inferred as the experimentally derived melting curves of the two strands of the DNA heteroduplexes increasingly diverge. RESULTS: COMA was successfully applied to the genetic classification of HIV-1 and HCV strains into phylogenetic lineages or subtypes. CONCLUSIONS: Use of this assay should accelerate current efforts to understand the global molecular epidemiology of HIV-1 and HCV and may extend to the genetic characterization of other genetically diverse infectious pathogens associated with numerous diseases.     

Unfolding of the tRNA(Phe) structure by complementary oligonucleotides

The effect of ribonuclease and cytochrome c on electrophoretic mobility of liposomes composed of phosphatidylcholine and diphosphatidylglycerol has been studied. zeta-Potential of lipid vesicles was found to decrease in the presence of proteins. Parameters of proteins binding to phospholipids were evaluated from the changes of surface charge density of model membranes. The constants of protein association with phospholipids were calculated to be about 4 x 10(4) M-1 for ribonuclease and about 5.4 x 10(4) M-1 for cytochrome c.     

Imitation of the sequential structure of actions by chimpanzees (Pan troglodytes)

Based on the assumption that glutathione peroxidase (GPx) activity might be limiting in preventing peroxide-induced impairment of endothelial regulatory functions, we studied the effect of a series of new selenium-containing GPx mimics on endothelial cells exposed to an inflammatory stress. The two compounds that have the highest GPx activity, BXT-51072 and BXT-51077, were shown to be the most efficient inhibitors of leukocyte recruitment by human umbilical vein endothelial cells (HUVEC), upon incubation with neutrophils (10-fold excess over HUVEC) and with 1 ng/ml TNF-alpha for 1 or 3.5 h. When HUVEC were pre- and cotreated with 10 microM of either compound, neutrophil adhesion and endothelial alteration were markedly inhibited, as assessed by immunoassays of myeloperoxidase and von Willebrand factor, respectively. These two GPx mimics were also found to be the most efficient inhibitors of the TNFalpha-induced endothelial expression of P- and E-selectin and of the TNFalpha- or interleukin1-induced endothelial release of interleukin-8. Our results demonstrate that GPx mimics such as BXT-51072 behave as potent antagonists of TNF-alpha and interleukin-1 through the downregulation of endothelial proinflammatory responses.     

Protein structure prediction by threading methods: evaluation of current techniques

This paper evaluates the results of a protein structure prediction contest. The predictions were made using threading procedures, which employ techniques for aligning sequences with 3D structures to select the correct fold of a given sequence from a set of alternatives. Nine different teams submitted 86 predictions, on a total of 21 target proteins with little or no sequence homology to proteins of known structure. The 3D structures of these proteins were newly determined by experimental methods, but not yet published or otherwise available to the predictors. The predictions, made from the amino acid sequence alone, thus represent a genuine test of the current performance of threading methods. Only a subset of all the predictions is evaluated here. It corresponds to the 44 predictions submitted for the 11 target proteins seen to adopt known folds. The predictions for the remaining 10 proteins were not analyzed, although weak similarities with known folds may also exist in these proteins. We find that threading methods are capable of identifying the correct fold in many cases, but not reliably enough as yet. Every team predicts correctly a different set of targets, with virtually all targets predicted correctly by at least one team. Also, common folds such as TIM barrels are recognized more readily than folds with only a few known examples. However, quite surprisingly, the quality of the sequence-structure alignments, corresponding to correctly recognized folds, is generally very poor, as judged by comparison with the corresponding 3D structure alignments. Thus, threading can presently not be relied upon to derive a detailed 3D model from the amino acid sequence. This raises a very intriguing question: how is fold recognition achieved? Our analysis suggests that it may be achieved because threading procedures maximize hydrophobic interactions in the protein core, and are reasonably good at recognizing local secondary structure.     

Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments

A number of methods exist for the prediction of protein secondary structure from primary sequence. One method identifies variable charged and conserved hydrophobic residues within large multiple alignments as a means of indicating outside and inside sites respectively in the protein structure. These sites are then manually fitted to secondary structure templates to generate a secondary structure prediction. Using the existing theoretical bases of this method, we present an algorithm (STAMA) which automatically carries out the initial variation/conservation analysis of the alignment. We also test the accuracy of complete predictions carried out by manual fitting of the STAMA-derived assignments to structure templates, using five large multiple alignments each including a protein of known structure. The method was found on average to predict only 57% of residues in the correct secondary structure, and was only as accurate as predictions carried out using the established and automated method of Garnier, Osguthorpe and Robson (1978) applied to a single sequence. When used in conjunction with other secondary structure prediction methods, however, the resulting consensus predictions were found to be very accurate, with 78% of the elements (alpha helices or beta strands) for which a consensus could be obtained being predicted correctly. The algorithm presented here, plus the assessment of the accuracy of prediction generated by this method, should enable this predictive approach to receive informed general use.     

Coronary restenosis after optimal (stent-like) initial angiographic results obtained by traditional balloon angioplasty

BACKGROUND AND OBJECTIVE: Elective native coronary artery stenting has shown its efficacy in lowering restenosis rates (RR) usually occurring after balloon angioplasty (PTCA). However ability of conventional PTCA to consistently provide low RR, through the achievement of large acute stent-like angiographic results, has not been investigated. This study was conducted to: (1) assess ability of optimal initial dilatation (OID), defined by residual lumen narrowing < or = 20%, significantly reduce current high RR following traditional PTCA; (2) evaluate the efficacy of OID obtainable by conventional PTCA in influencing adverse effects of single variables predisposing to restenosis. METHODS: Of consecutive 601 patients who underwent PTCA, 569 (94.6%), 483 men and 86 women, aged 38-76 years, had a successful procedure on 645/678 lesions (95.1%). After a plaque fracture was obtained by the first inflation, step-increases in pressure of 1 atm and 60 second-inflation-times were applied, until a large lumen (the nearest to normal) and smooth contours were seen, or any wall damage detected by using step-by-step angiographic tests. Acute optimal results (group A) were 450 (69.7%) and sub-optimal results (group B) were 203 (30.3%). After a mean time of 9 +/- 1.8 months, 543 patients (95.4%) had angiographic restudy on 611 (94.7%) successfully treated lesions. RESULTS: Restenosis (> 50% stenosis at restudy) occurred in 27.1% of patients and in 24.5% of lesions. RR was 18.8% in group A and 37.8% in group B (p < 0.0001). Significant lower RR were observed in group A in comparison with group B, for single variables examined, except for length > 10 mm. By multivariate analysis of all treated lesions, sub-optimal initial dilatation, unstable angina, lesion length > 10 mm and eccentricity emerged as major determinants of restenosis. Following OID only length > 10 mm was highly predictive of this event and, in the absence of this adverse variable, RR was only 13.6%. CONCLUSION: Counterbalancing adverse effects of many variables predisposing to restenosis, OID obtained by traditional PTCA seem to significantly reduce the risk of recurrence, particularly in lesions no longer than 10 mm.     

Development of a capillary electrophoretic separation of an N-(substituted)-glycine-peptoid combinatorial mixture

Conversion of the noninfectious, cellular form of the scrapie prion (PrPC) to the infectious form (PrPSc) is thought to be driven by an alpha-helical to beta-sheet conformational transition. The N-truncated polypeptide PrP27-30, which encompasses residues 90-231 of PrPSc and from which the truncated peptide is derived by limited proteolysis, assembles into amyloid rods that are rich in the beta-sheet conformation. The N-terminal half of PrP27-30, which includes residues 90-145 of PrP (SHa90-145) and contains the two putative alpha-helical domains H1 (PrP109-122) and H2 (PrP129-141), appears to be particularly crucial in the alpha --> beta conversion. To assess their role in this conformational transition, we have analyzed in detail X-ray diffraction patterns from the prion-related peptides A8A (PrP113-120), H1, and SHa90-145. We used iterative Fourier synthesis with beta-silk as an initial model for assigning phases. For H1, the lyophilized and acetonitrile-solubilized/dehydrated specimens gave two different electron density maps. The former showed that the beta-sheets were composed of small side chains as in A8A. The latter showed two types of beta-sheets having smaller and larger side chains, suggesting a turn. Such a turn was not observed in the lyophilized H1, indicating that the internal turn in H1 depends on the physical-chemical environment. In SHa90-145, the beta-chains are assembled in approximately 40 A-wide crystal domains (termed beta-crystallites), and the electron density maps of these crystallites showed evidence for turns within both the H1 and H2 domains. The molecular folding of H1-H2 is compared here with the recent NMR solution structure of recombinant hamster prion, and the effect of pH on the conformational change is discussed. The most compact structure based on the X-ray diffraction analysis showed that the N-terminal, smaller residues of H2 fold back and are hydrogen-bonded with the C-terminal, smaller residues of H1. Similar folding is observed in the NMR solution structure. Comparison of the NMR structures at different pH with the X-ray diffraction results suggests that histidine and lysine residues in the N-terminal sequence of PrP may figure in the alpha --> beta structure transition of PrP.