Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.     

Change in optic disk topography after trabeculectomy

PURPOSE: To investigate the relationship between optic disk topography and intraocular pressure before and after trabeculectomy with confocal scanning laser ophthalmoscopy. METHODS: The eyes of 49 consecutive patients undergoing trabeculectomy at a university-based glaucoma practice underwent preoperative and postoperative imaging using a confocal scanning laser ophthalmoscope (Heidelberg Retina Tomograph). Three images of one eye of each patient were obtained with a 15-degree field of view. Preoperative images were obtained approximately 2 months before surgery (mean +/- SD, 2.4 +/- 1.6 months). Postoperative images were obtained at least 3 months after surgery (mean, 4.5 +/- 2.6 months). RESULTS: Mean preoperative intraocular pressure, postoperative intraocular pressure, and percent change in intraocular pressure respectively were 23.1 +/- 6.8 mm Hg, 12.7 +/- 7.1 mm Hg, and 43.8% +/- 29.9%. A significant association (P < .01) was found between percent decrease in intraocular pressure and decreases in cup area, cup volume, and cup/disk area ratio as well as between percent decrease in intraocular pressure and increases in rim area, rim volume, mean height contour, retinal cross-section area, and height in contour. Between 11.7% and 31.2% of the variability (R2) in these parameters was explained by the percent change in intraocular pressure. Topography changes were more strongly associated with percent change than with mean change in intraocular pressure. We found no association between percent decrease in intraocular pressure and reference plane height or maximum cup depth. CONCLUSIONS: Changes in optic nerve topography were associated with reduction in intraocular pressure after trabeculectomy.     

Analysis of linkage between beta-lactoglobulin and J blood group system loci in cattle

Linkage between loci controlling variants of beta-lactoglobulin and blood groups of the J system in cattle was studied by means of stochastic genetic methods reported earlier. The studies were conducted on a herd of Black Pied cattle improved with Holstein sires; population genetic data were analyzed. A plot for lod score was constructed, and point (r - 0.28) and interval estimations of the coefficient of recombination were obtained. The results are in good agreement with earlier reported data on other subjects.     

Surgery for primary hyperparathyroidism 1962-1996: indications and outcomes

Twenty-two cases of ameloblastoma and ten cases of adenomatoid odontogenic tumour (AOT) were analyzed comparatively by the AgNOR technique. Ameloblastomas were distributed into three groups according to their clinical behaviour: primary lesions without recurrences (PLWTR), 5 cases; primary lesions with recurrences (PLWR), 4 cases; and recurrences, 13 cases. The cases were also regrouped according to their histological pattern: follicular (9 cases), plexiform (7 cases), acanthomatous (4 cases) and unicystic (2 cases). Considering histological patterns, there was a significant statistical difference only between follicular and plexiform types. There were no significant differences between the group of ameloblastomas and the group of AOTs or between the three groups of ameloblastomas with different clinical behaviour. Our results strongly suggest that the distinct clinical behaviour of ameloblastomas and AOT is not correlated with their cellular proliferation ratio. Thus, the infiltrative ability of the ameloblastomas is probably not related to the cellular proliferation index of these tumours.     

Antithrombins Wibble and Wobble (T85M/K): archetypal conformational diseases with in vivo latent-transition, thrombosis, and heparin activation

The inherent variability of conformational diseases is demonstrated by two families with different mutations of the same conserved aminoacid in antithrombin. Threonine 85 underlies the opening of the main beta-sheet of the molecule and its replacement, by the polar lysine, in antithrombin Wobble, resulted in a plasma deficiency of antithrombin with an uncharacteristically severe onset of thrombosis at 10 years of age, whereas the replacement of the same residue by a nonpolar methionine, antithrombin Wibble, gave near-normal levels of plasma antithrombin and more typical adult thromboembolic disease. Isolated antithrombin Wibble had a decreased thermal stability (Tm 56.2, normal 57.6 degreesC) but was fully stabilized by the heparin pentasaccharide (Tm 71.8, normal 71.0 degreesC), indicating that the prime abnormality is a laxity in the transition of the main sheet of the molecule from the 5- to 6-stranded form, as was confirmed by the ready conversion of antithrombin Wibble to the 6-stranded latent form on incubation. That this transition can occur in vivo was shown by the finding of nearly 10% of the proband's plasma antithrombin in the latent form and also, surprisingly, of small but definitive amounts of latent antithrombin in normal plasma. The latent transition will be predictably accelerated not only by gross mutations, as with antithrombin Wobble, to give severe episodic thrombosis, but also by milder mutations, as with antithrombin Wibble, to trigger thrombosis in the presence of other predisposing factors, including the conformational stress imposed by the raised body temperatures of fevers. Both antithrombin variants had an exceptional (25-fold) increase in heparin affinity and this, together with an increased inhibitory activity against factor Xa, provides evidence of the direct linkage of A-sheet opening to the conformational basis of heparin binding and activation.     

Enzymes harboring unnatural amino acids: mechanistic and structural analysis of the enhanced catalytic activity of a glutathione transferase containing 5-fluorotryptophan

The catalytic characteristics and structure of the M1-1 isoenzyme of rat glutathione (GSH) transferase in which all four tryptophan residues in each monomer are replaced with 5-fluorotryptophan are described. The fluorine-for-hydrogen substitution does not change the interaction of the enzyme with GSH even though two tryptophan residues (Trp7 and Trp45) are involved in direct hydrogen-bonding interactions with the substrate. The rate constants for association and dissociation of the peptide, measured by stopped-flow spectrometry, remain unchanged by the unnatural amino acid. The 5-FTrp-substituted enzyme exhibits a kcat of 73 s-1 as compared to 18 s-1 for the native enzyme toward 1-chloro-2,4-dinitrobenzene. That the increase in the turnover number is due to an enhanced rate of product release in the mutant is confirmed by the kinetics of the approach to equilibrium for binding of the product. The crystal structure of the 5-FTrp-containing enzyme was solved at a resolution of 2.0 A by difference Fourier techniques. The structure reveals local conformational changes in the structural elements that define the approach to the active site which are attributed to steric interactions of the fluorine atoms associated with 5-FTrp146 and 5-FTrp214 in domain II. These changes appear to result in the enhanced rate of product release. This structure represents the first of a protein substituted with 5-fluorotryptophan.     

Simulation of gas–solid two-phase flow in the annulus of drilling well

This paper investigates the hydrodynamic behavior of gas–solid two-phase flow in the annular space of an air drilling well under different arrangements by using three-dimensional approach. Two-fluid model is used to solve the governing equations in the Eulerian–Eulerian framework. Effect of eccentricity and drill pipe rotation on the pressure drop, volume fraction and velocity profile are examined. The results are compared with available data in the literature and good agreement is found. The results show that the presence of solid particles in the annulus change the air velocity profile significantly and create two off-center peaks velocity close to the walls instead of one peak velocity in the middle. Eccentricity of drill pipe makes more accumulation of the cuttings in the smaller space of the annulus. Increasing the eccentricity increases pressure drop due to impact of particles with annulus wall and also particles collision with each other. Rotation of the drill pipe shifts maximum air velocity location toward smaller space of the annulus which results more uniform cutting distributions in the annulus and improvement in their transportations. Pressure drop in the annulus increases as eccentricity and rotation of drill pipe increase.     

Lu3+/Yb3+ and Lu3+/Er3+ co-doped antimony selenide nanomaterials: synthesis,characterization, and electrical,thermoelectrical, and optical properties

Lu³⁺/Yb³⁺ and Lu³⁺/Er³⁺ co-doped Sb₂Se₃ nanomaterials were synthesized by co-reduction method in hydrothermal condition. Powder X-ray diffraction patterns indicate that the Ln_xLn^′_xSb_2−2xSe₃ Ln: Lu³⁺/Yb³⁺ and Lu³⁺/Er³⁺ crystals (x = 0.00 − 0.04) are isostructural with Sb₂Se₃. The cell parameters were increased for compounds upon increasing the dopant content (x). Scanning electron microscopy and transmission electron microscopy images show that co-doping of Lu³⁺/Yb³⁺ ions in the lattice of Sb₂Se₃ produces nanorods, while that in Lu³⁺/Er³⁺ produces nanoparticles, respectively. The electrical conductivity of co-doped Sb₂Se₃ is higher than that of the pure Sb₂Se₃ and increases with temperature. By increasing the concentration of Ln³⁺ions, the absorption spectrum of Sb₂Se₃ shows red shifts and some intensity changes. In addition to the characteristic red emission peaks of Sb₂Se₃, emission spectra of co-doped materials show other emission bands originating from f-f transitions of the Yb³⁺ ions.     

New Flower-Shaped Lead(II) Coordination Polymer at the Nano Scale: Synthesis, Structural Characterization and DFT Calculations of [Pb(o-phen)(N3)2] n Containing the Pb-(μ1,1-N3)(μ1,3-N3) Motif

A new nano-flower lead(II) azido coordination polymer from the ligand, orthophenanthroline (o-phen), [Pb(o-phen)(μ_1,1-N₃)(μ_1,3-N₃)] _n (1), was synthesized by a sonochemical method. Compound 1 was characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), elemental analyses and IR spectroscopy. Single crystalline material was obtained using a heat gradient applied to a solution of the reagents. The structure of 1 is a coordination polymer of lead(II) containing the Pb-(μ_1,1-N₃)(μ_1,3-N₃) motif, formed of one-dimensional chains. The structure of the 1 was optimized by density functional theory. Structural parameters and IR spectra for 1 are consistent with the crystal structure. Pure phase PbO nanoparticles were obtained by thermolysis of 1 with oleic acid as a surfactant at 180 and 200 °C an air. PbO nanoparticles were characterized by XRD and SEM.     

Sonochemical Synthesis and Characterization of A Nano-Rod Lead(II) Supramolecular, Three Dimensional Coordination Compound: New Precursor to Produce Pure Phase Nano-Sized Lead(II) Oxide

Nanorods of a lead(II) supramolecular three-dimensional (3D) coordination compound, [Pb(tfpb)₂]_n (1) (Htfpb?=?4,4,4-trifluoro-1-phenyl-1,3-butanedione), was prepared by the sonochemical method. The new nano-structure was characterized by scanning electron microscopy, X-ray powder diffraction, elemental analyses and IR spectroscopy. A single-crystal structure of the compound showed that the coordination number of Pb(II) is eight with six O-donor atoms from the tfpb ligand and two F-donors from anionic ligands. The 3D supramolecular structure of 1 is realized by weak directional C–F···F–C and π–π stacking interactions. After calcination of nano-sized 1 at 500?°C, pure phase nano-sized lead(II) oxide is produced.