Identification of a new high-affinity binding protein for neurotoxic phospholipases A2

We have examined the relationship between the procoagulant activity of F3II mouse mammary carcinoma cells and the production of urokinase, a profibrinolytic serine protease involved in tumor invasion and hematogenous metastasis. F3II cells were capable of inducing the conversion of purified fibrinogen to fibrin in the presence of calcium and plasma traces. Immunocytochemical examination of semi-confluent monolayers demonstrated that F3II cells also synthesized high levels of urokinase. Although fibrinogen did not modify profibrinolytic activity produced by F3II monolayers, fibrin formation increased tumor-derived urokinase activity by two-fold. The present data provide new insights into the cooperative role of coagulation and fibrinolysis facilitating and perpetuating tumor invasion.     

Validity, predictive efficiency, and practical significance of selection tests.

The acceptance of validity coefficients at face value as measures of practical significance is evaluated by examining each functional relationship between 3 indexes of predictive efficiency r, r2, and E and 3 measures of practical significance the increase of the criterion mean, the expected proportion "satisfactory," and the expected proportion in 10 criterion categories. The validity coefficient, r is a linear function of the increase of the criterion mean and very nearly a linear function of the other 2 measures of practical significance; r2 and E are related to these 3 measures in a more curvilinear manner. A table is presented that gives the proportion expected in each of 18 criterion categories as a function of r and the selection ratio. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Prediction and evaluation of side-chain conformations for protein backbone structures

A common approach to protein modeling is to propose a backbone structure based on homology or threading and then to attempt to build side chains onto this backbone. A fast algorithm using the simple criteria of atomic overlap and overall rotamer probability is proposed for this purpose. The method was first tested in the context of exhaustive searches of side chain configuration space in protein cores and was then applied to all side chains in 49 proteins of known structure, using simulated annealing to sample space. The latter procedure obtains the correct rotamer for 57% and the correct chi 1 value for 74% of the 6751 residues in the sample. When low-temperature Monte-Carlo simulations are initiated from the results of the simulated-annealing processes, consensus configurations are obtained which exhibit slightly more accurate predictions. The Monte-Carlo procedure also allows converged side chain entropies to be calculated for all residues. These prove to be accurate indicators of prediction reliability. For example, the correct rotamer is obtained for 79% and the correct chi 1 value is obtained for 84% of the half of the sample residues exhibiting the lowest entropies. Side chain entropy and predictability are nearly completely uncorrelated with solvent-accessible area. Some precedents for and implications of this observation are discussed.     

The calculation of habit planes for elastic transformations by minimization of their elastic strain energy

By using Eshelby’s method for the determination of the stresses and strains generated in a transformation, the shape and orientation of an ellipsoidal region of transformed phase that minimizes the elastic strain energy accompanying the transformation are calculated together with the change in elastic strain energy. The orientation of minimum total energy describes the habit plane. The applicability of the approach is demonstrated by showing that the habit planes of twins in cubic crystals, and martensitic plates in In-20 pct TI and Fe-31 pct Ni, which have been calculated by other methods, can alternatively be determined by this method. It is then used to calculate that the habit plane for martensitic plates in bulk, high density, oriented orthorhombic polyethylene should be (4.67,1,0) orthorhombic. As a consequence of these calculations it is shown that minimization of the total elastic strain energy must be the dominating factor in the nucleation event of transformed products in most metals.     

Search for chlorinated sesquiterpene lactones in the neurotoxic thistle Centaurea solstitialis by liquid chromatography-mass spectrometry, and model studies on their possible artifactual formation

An HPLC method has been developed for the analysis of sesquiterpene lactones of the neurotoxic plant Centaurea solstitialis (Asteraceae). The presence of sesquiterpene lactone chlorohydrins in extracts was investigated by means of liquid chromatography-thermospray mass spectrometry. In contrast to earlier reports of a series of mono- and dichlorohydrins from this plant, traces only of two monochlorohydrins could be detected in lipophilic extracts. Model studies carried out with extracts and with the genuine sesquiterpene diepoxide repin and its epimer subluteolide showed that (i) monochlorohydrins can be formed in CHCl3 under usual laboratory conditions; (ii) the epoxide moiety at C-4 of the sesquiterpenes is extremely labile, reacting immediately and quantitatively with traces of HCl to the corresponding monohydrins; (iii) epoxide ring opening at the acyl side chain occurs only at higher HCl concentrations. Confirmation of the peak identity was obtained by the isotope ratio of chlorinated compounds and comparison with authentic samples. The structures of the mono- and dichlorohydrins were established by NMR spectroscopy.     

The calculation of habit planes for elastic transformations by minimization of their elastic strain energy

By using Eshelby's method for the determination of the stresses and strains generated in a transformation, the shape and orientation of an ellipsoidal region of transformed phase that minimizes the elastic strain energy accompanying the transformation are calculated together with the change in elastic strain energy. The orientation of minimum total energy describes the habit plane. The applicability of the approach is demonstrated by showing that the habit planes of twins in cubic crystals, and martensitic plates in In-20 pct Tl and Fe-31 pct Ni, which have been calculated by other methods, can alternatively be determined by this method. It is then used to calculate that the habit plane for martensitic plates in bulk, high density, oriented orthorhombic polyethylene should be (4.67,1,0) orthorhombic- As a consequence of these calculations it is shown that minimization of the total elastic strain energy must be the dominating factor in the nucleation event of transformed products in most metals.     

Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics

An N-acetyl-2-aminofluorene (AAF) modified deoxyoligonucleotide duplex, d(C1-C2-A3-C4-[AAF-G5]-C6-A7-C8-C9).d(G10-G11-T12-G13-C14-++ +G15-T16-G17-G18), was studied by one- and two-dimensional NMR spectroscopy. Eight of the nine complementary nucleotides form Watson-Crick base pairs, as shown by NOEs between the guanine imino proton and cytosine amino protons for G.C base pairs or by an NOE between the thymine imino proton and adenine H2 proton for A.T base pairs. The AAF-G5 and C14 bases show no evidence of complementary hydrogen bond formation to each other. The AAF-G5 base adopts a syn conformation, as indicated by NOEs between the G5 imino proton and the A3-H3' and A3-H2'/H2" protons and by NOEs between the fluorene-H1 proton of AAF and the G5-H1' or C6-H1' proton. The NOEs from the C4-H6 proton to C4 sugar protons are weak, and thus the glycosidic torsion angle in this nucleotide is not well defined by these NMR data. The remaining bases are in the anti conformation, as depicted by the relative magnitude of the H8/H6 to H2' NOEs when compared to the H8/H6 to H1' NOEs. The three base pairs on each end of the duplex exhibit NOEs characteristic of right-handed B-form DNA. Distance restraints obtained from NOESY data recorded at 32 degrees C using a 100-ms mixing time were used in conformational searches by molecular mechanics energy minimization studies. The final, unrestrained, minimum-energy conformation was then used as input for an unrestrained molecular dynamics simulation. Chemical exchange cross peaks are observed, and thus the AAF-9-mer exists in more than a single conformation on the NMR time scale. The NMR data, however, indicate the presence of a predominant conformation (> or = 70%). The structure of the predominant conformation of the AAF-9-mer shows stacking of the fluorene moiety on an adjacent base pair, exhibiting features of the base-displacement [Grunberger, D., Nelson, J. H., et al. (1970) Proc. Natl. Acad. Sci. U.S.A. 66, 488-494] and insertion-denaturation models [Fuchs, R.P.P., & Daune, M. (1971) FEBS Lett. 14, 206-208], while the distal ring of the fluorene moiety protrudes into the minor groove.     

Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures

The normal mode analysis of human hemoglobin showed the presence in the deoxy T-state of one main preferential direction that brings the structure close to the R-state, with a low-energy variation, while in the oxy R-state there are several modes that point towards the T-state, but with higher energy variations and less contribution to the transition. The displacement along a combination of normal modes, followed by energy minimization, starting from the R-state, did not allow one to obtain a structure significantly different from that of R, showing that the fully oxygenated hemoglobin is trapped in a deep and narrow potential energy minimum. On the contrary, starting from the deoxy T-state, the displacement along a combination of normal modes, followed by energy minimization, yielded an intermediate structure, that we designate Tmin(d1), which is closer to R; the normal modes of Tmin(d1) indicated that the potential energy minimum in the vicinity of this structure is as narrow as that of R but less deep. The procedure of displacement along the modes, followed by energy minimization, was applied to Tmin(d1), yielding Tmin(d2); then the procedure was repeated, yielding the intermediate structures Tmin(d3) and Tmin(d4). The structures Tmin(d2), Tmin(d3) and Tmin(d4) are not significantly different from each other, indicating that they are trapped in a narrow, deep energy minimum. This procedure revealed the existence of at least two intermediate sets of structures between T and R: the first one, Tmin(d1), is different from the T and R structures, while the second set, Tmin(d2), Tmin(d3) and Tmin(d4), is quaternary R-like and tertiary T-like, where the contacts at the interfaces alpha1 beta1 and alpha1 beta2 are R-like, and the alpha and beta heme environments are still T-like.     

Cell density-sensing in Dictyostelium by means of the accumulation rate, diffusion coefficient and activity threshold of a protein secreted by starved cells

The simple eukaryote Dictyostelium discoideum grows as an amoeba on leaf and soil surfaces. When starved, the amoebae aggregate and differentiate. The amoebae can also be induced to differentiate as isolated cells submerged in buffer, if the buffer contains a sufficiently high concentration of a protein (CMF) secreted by starved cells. CMF is also necessary for aggregation and differentiation on surfaces. This indicated that CMF has either an autocrine function or is part of a density-sensing system. To distinguish between these two possible functions, we first examined the rate at which CMF is accumulated and the activity threshold of cells for CMF, since both parameters will affect whether a cell can provide enough CMF to self-stimulate. We find that CMF potentiates its own accumulation, and that otherwise the accumulation rate and activity threshold are affected very little by a variety of physiological conditions. We then use diffusion calculations to show that even after many hours of continuous secretion, the CMF concentration adjacent to an isolated starved cell on a leaf or soil surface will be too low to allow differentiation, whereas an extracellular concentration of CMF sufficiently high to allow differentiation will occur when starved cells are at high densities. We find a close match between the predicted and experimentally observed density necessary for differentiation. The theoretical and observed behavior of cells at different cell densities suggests that due to its accumulation rate, diffusion coefficient, and activation threshold, CMF can function as part of a cell density-sensing system which allows Dictyostelium cells in the wild to co-ordinate their development.     

A further attempt to differentiate violent from nonviolent offenders by means of a battery of psychological tests.

30 male Ss who had been convicted of violent offenses and 30 convicted on nonviolent offenses (mean ages 17.5 and 17.4 yrs, respectively) were administered the WAIS, Buss-Durkee Hostility Inventory (BDHI), the Hostility and Direction of Hostility Questionnaire, and the Eysenck Personality Questionnaire. Only 6 of the dependent variables differentiated between the 2 groups at or beyond the .05 level of significance. They were Information, Comprehension, Verbal IQ, Object Assembly, Full Scale IQ, and Assault. With the exception of Assault (a BDHI subscale), all the variables come from the WAIS. There were no significant differences between the 2 groups on S. B. Eysenck and H. J. Eysenck's (1975) personality dimensions of extraversion, neuroticism, and psychoticism. (French abstract) (27 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Utilization and predictive value of laboratory tests in patients referred to rheumatologists by primary care physicians

OBJECTIVE: Antinuclear antibodies (ANA), rheumatoid factors (RF), and erythrocyte sedimentation rate (ESR) are among the most frequently requested tests in the diagnosis and investigation of connective tissue diseases (CTD). We evaluate the utilization patterns and predictive value of these tests in patients referred to rheumatologists by primary care physicians. METHODS: We reviewed the records of all new patients referred by primary care physicians in 1994 to 2 rheumatologists practicing at the University of Alberta. Data extracted from the records included diagnostic tests requested by referring primary care physicians, signs and symptoms at the initial rheumatology consult, and followup diagnoses. RESULTS: Seven hundred eleven new patients had been referred by over 300 primary care physicians: RF had been requested in 25%, ANA in 21%, and ESR in 29%. One hundred nine (15%) of the 711 patients had a CTD, 45 (6%) had rheumatoid arthritis (RA), and 8 (1%) systemic lupus erythematosus (SLE). The predictive values of positive tests for the diagnosis of CTD were low: 49% for RF, 29% for ANA, and 35% for ESR. For RA, the positive predictive values were 44% for RF, 8% for ANA, 17% for ESR; for SLE, 2, 12, and 3%, respectively. Diffuse musculoskeletal pain and fatigue were significantly associated with test utilization, although most patients with these symptoms had fibromyalgia or localized soft tissue rheumatism. CONCLUSION: Primary care physicians frequently requested autoantibodies in patients referred to rheumatologists. Most tests were negative, and were often requested in patients without CTD, resulting in low positive predictive values and questionable clinical utility. These findings suggest inappropriate overuse and lack of understanding of the use of autoantibody tests in diagnosing rheumatic diseases. A decrease in inappropriate use could be achieved by emphasizing that fatigue and diffuse musculoskeletal pain are not indicative of CTD in the absence of other features such as joint swelling, typical rash, or organ involvement.     

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill (1985), which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail (1996a) gave approximation algorithms for folding proteins on the cubic lattice under the HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that the triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.     

Spectral diffusion and the energy landscape of a protein

We present a novel type of spectral diffusion experiment in the millikelvin range to characterize the energy landscape of a protein as compared with that of a glass. We measure the time evolution of spectral holes for more than 300 hr after well-defined initial nonequilibrium conditions. We show that the model of noninteracting two-level systems can describe spectral diffusion in the glass, but fails for the protein. Our results further demonstrate that randomness in the energy landscape of a protein shows features of organization. There are "deep minimum" states separated by barriers, the heights of which we are able to estimate. The energy landscape of a glass is featureless by comparison.     

Differential diagnosis of ischemic heart disease and cardialgia by means of pharmacological tests in the polyclinical practice

The possibility of differential diagnosis of ischemic heart disease and cardialgia at a polyclinic is analyzed. A total of 1110 patients with a preliminary diagnosis of ischemic heart disease were examined. In 214 of them the data gathered during many years of observations have cast doubt on the validity of this diagnosis. The patients of this group were made to undergo tests with potassium chloride and obsidan. Subject to appraisal were the ECG reaction and an analysis of angular variations of the vectors in the terminal portion of the ventricular complex. The described tests were shown to help determine the significance of "functional" or "organic" changes of the myocardium in the genesis of repolarizational ECG perturbances.