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.     

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.     

Perimetric motion thresholds are elevated in glaucoma suspects and glaucoma patients

The purpose of this study was to determine if a clinically feasible perimetric motion test utilizing random-dot kinematograms could identify glaucomatous visual field defects. Using a staircase procedure, an automated perimetric motion test and a larger foveally presented target were given to normal (n = 30), glaucoma suspects (n = 31) and primary open-angle glaucoma patients (n = 19). Motion thresholds at specific locations throughout the whole visual field were significantly elevated in glaucoma patients (P < or = 0.001). Perimetric motion testing identified 84.2% of the primary open-angle glaucoma patients and 25.8% of the glaucoma suspects as abnormal. A larger foveal stimulus was unable to distinguish between the different subject groups (P < or = 0.185). Perimetric motion thresholds were significantly correlated with Humphrey standard visual field thresholds in the glaucoma and glaucoma-suspect patients (P < or = 0.0002).     

Integrated services for treatment of schizophrenic substance abusers: demographics, symptoms, and substance abuse patterns

We have previously described a model of outpatient integrated treatment for patients with comorbid psychoactive substance use disorders and schizophrenia (PSUD/S)(1). Here we review relevant literature on comorbidity and outline the rationale for integrated services. Further, we describe results from 3 related studies: First, we document the approximate incidence of PSUD among a heterogeneous group of 602 schizophrenic inpatient admissions to our hospital. Second, we describe in greater detail the psychiatric symptoms and patterns of substance abuse among a subsample of 106 inpatients with PSUD/S, contrasting them with 112 patients with PSUD and mixed psychotic disorders, but who are not schizophrenic. Third, we present a prospective research project and describe a sample of 30 patients with PSUD/S, detailing demographic characteristics, psychiatric symptoms and substance abuse history. Attention is given to current issues in the differential diagnosis of patients with PSUD/S using standardized instruments.     

Acral lentiginous melanoma

BACKGROUND: Ossification of the posterior longitudinal ligament (OPLL) may cause neuropathic bladder dysfunction due to spinal cord involvement. OPLL, unlike a traumatic spinal cord lesion, progresses insidiously and sometimes affects longer cord segments. As the manifestation of bladder dysfunction may depend on the development of OPLL, we studied the relationship between bladder function and roentgenographic changes in the spinal canals of OPLL patients. PATIENTS AND METHODS: Eighteen surgical candidates (11 males and 7 females, 34 to 85 years old) were studied urodynamically. Sixteen underwent CO2-filling cystometry, uroflowmetry and measurement of their residual urine volume. Cystometry was omitted in the remaining 2 patients. The vertical extent of OPLL and the degree of stenosis in the spinal canal was estimated by x-ray films and CT. RESULTS: The cystometric study revealed detrusor hyperreflexia in 2 patients and areflexic or underactive detrusors in 5 patients. Intermittent flows or considerable amounts of residual urine were also observed in the arefilexia/underactive group. Uroflowmetry showed a normal flow with little residual urine in both patients in whom cystometry was omitted. Bladder sensation was maintained in all patients. The occurrence of abnormal detrusor activity had no relationship to the degree of canal stenosis, while the occurrence of an areflexic or underactive detrusor correlated with the vertical extent of OPLL. CONCLUSION: Although detrusor hyperreflexia is common in an upper spinal cord lesion, attention should also be paid to the development of detrusor underactivity in patients with a wide vertical extent of OPLL.     

Molecular characterization of Borrelia burgdorferi sensu lato from Slovenia revealing significant differences between tick and human isolates

The aim of the study was to evaluate the morphological and functional status of the liver in acute, oral cholinesterase inhibitors poisoning using static scintigraphy, hepatography and measurements of chosen enzymes activity. Considering the different clinical picture of cholinesterase inhibitors poisonings in people, it was necessary to estimate the poisoning severity and its dependence on the frequency and intensification of the liver lesion. Under examination there were 37 cholinesterase inhibitors orally poisoned patients, treated at the Department of Toxicology in the years 1992-1995. The examined group comprised 7 women (19%) and 30 men (81%). Organophosphate compounds poisoning was noted in 14 patients, and carbamates poisonings in 23 patients. The reference group comprised 30 healthy men aged 24 to 59 years not exposed to hepatotoxic agents. More than 90% of patients were classified as severe poisoned. Any fatal case was not noted. A differently intensified pathological changes of the liver dependent on age and poisoning severity were found in 97.2% of patients and their frequency was significantly higher than in the control group. Hepatographic picture revealed in 96.6% of cases the liver lesion. Hepatographic picture of the liver was also dependent on poisoning severity. The higher activity of AST, ALT, AP and higher bilirubin concentration in blood were noted in poisoned men compared to the control group. Control scintigraphic examination revealed a considerable improvement in the intensification of the liver scintigraphic picture in 40% of the patients and a higher intensification in 13% of the subjects. In 46.6% of the patients the intensification of scintigraphic changes remained at the same level. Considering arbitrary criteria for the degree of the liver lesion, the improvement in the intensification of hepatographic changes was noted in 42.8% of the patients; the intensification of the liver lesion was not noted even in one case. Analyzing the percentage of the liver lesion for each individual patient, improvement was noted in 92.8% of the examined patients, and the changes with the same level of intensification in 7.2%. Deterioration was not noted at all. Conclusion: The liver scintigraphy and hepatography combined with biochemical analysis allows to assess the liver condition in acute cholinesterase inhibitors poisoning.