The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory.

Magnesium ions play a crucial role in the structural integrity and biological activity of nucleic acids. Experimental thermodynamic descriptions of Mg(2+) interactions with nucleic acids in solution have generally relied on the analyses of binding polynomials to estimate the energetic contributions of diffuse and site-bound ions. However, since ion binding is dominated by long-range electrostatic forces, such models provide only a phenomenological description of the experimental Mg(2+) binding data and provide little insight into the actual mechanism of the binding equilibria. Here, we present a rigorous theoretical framework based on the non-linear Poisson-Boltzmann (NLPB) equation for understanding diffuse ion interactions that can be used to interpret experimental Mg(2+) binding isotherms. As intuitively expected, in the NLPB model binding is simply the total accumulation of the ion around the nucleic acid. Comparing the experimental data to the calculated curves shows that the NLPB equation provides a remarkably accurate description of Mg(2+) binding to linear polynucleotides like DNA and poly(A x U) without any fitted parameters. In particular, the NLPB model explains two general features of magnesium binding; the strong dependence on univalent salt concentration, and its substantial anticooperativity. Each of these effects can be explained by changes in the Mg(2+) distribution around the polyion under different solution conditions. In order to more fully understand these different aspects of magnesium binding, the free energy of Mg(2+) binding, DeltaGMg, is calculated and partitioned into several salt-dependent contributions: the change in the electrostatic interaction free energy of the charges, DeltaDeltaGE.D (including Mg(2+)-phosphate, Mg(2+)-Mg(2+), Mg(2+)-Na(+), Na(+)-Na(+), Na(+)-phosphate interactions, and similar contributions for Cl(-)) and the cratic free energies of (re)organizing the MgCl2 and NaCl atmospheres, DeltaG(Mg)org and DeltaDeltaG(Na)org, respectively. For the systems studied here, DeltaGMg is strongly influenced by entropic free energy changes in the distributions of both NaCl and MgCl2, DeltaG(Mg)org and DeltaDeltaG(Na)org. From this analysis, we also raise the possibility that coions added with the magnesium salt might play an important role in the overall stability of nucleic acids under some conditions.

Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

Our current understanding of Mg(2+) binding to RNA, in both thermodynamic and structural terms, is largely based on classical studies of transfer RNAs. Based on these studies, it is clear that magnesium ions are crucial for stabilizing the folded structure of tRNA. We present here a rigorous theoretical model based on the nonlinear Poisson-Boltzmann (NLPB) equation for understanding Mg(2+) binding to yeast tRNA(Phe). We use this model to interpret a variety of experimental Mg(2+) binding data. In particular, we find that the NLPB equation provides a remarkably accurate description of both the overall stoichiometry and the free energy of Mg(2+) binding to yeast tRNA(Phe) without any fitted parameters. In addition, the model accurately describes the interaction of Mg(2+) with localized regions of the RNA as determined by the pK(a) shift of differently bound fluorophores. In each case, we find that the model also reproduces the univalent salt-dependence and the anticooperativity of Mg(2+) binding. Our results lead us to a thermodynamic description of Mg(2+) binding to yeast tRNA(Phe) based on the NLPB equation. In this model, Mg(2+) binding is simply explained by an ensemble of ions distributed according to a Boltzmann weighted average of the mean electrostatic potential around the RNA. It appears that the entire ensemble of electrostatically bound ions superficially mimics a few strongly coordinated ions. In this regard, we find that Mg(2+) stabilizes the tertiary structure of yeast tRNA(Phe) in part by accumulating in regions of high negative electrostatic potential. These regions of Mg(2+) localization correspond to bound ions that are observed in the X-ray crystallographic structures of yeast tRNA(Phe). Based on our results and the available thermodynamic data, there is no evidence that specifically coordinated Mg ions have a significant role in stabilizing the native tertiary structure of yeast tRNA(Phe) in solution.

Salt effects on ligand-DNA binding. Minor groove binding antibiotics.

Salt dependent electrostatic effects play a central role in intermolecular interactions involving nucleic acids. In this paper, the finite-difference solution to the nonlinear Poisson-Boltzmann (NLPB) equation is used to evaluate the salt dependent contribution to the electrostatic binding free energy of the minor groove binding antibiotics DAPI, Hoechst 33258 and netropsin to DNA using detailed molecular structures of the complexes. For each of these systems, a treatment based on the NLPB equation accurately describes the variation of the experimentally observed binding constant with bulk salt concentration. A solvation formalism is developed in which salt effects are described in terms of three free energy contributions: the electrostatic ion-molecule interaction free energy, delta delta G degrees im; the electrostatic ion-ion interaction free energy, delta delta G degrees ii; and the entropic ion organization free energy, delta delta G degrees org. The electrostatic terms, delta delta G degrees im and delta delta G degrees ii, have both enthalpic and entropic components, while the term delta delta G degrees org is purely a cratic entropy. Each of these terms depends significantly on salt dependent changes in the counterion and coion concentrations around the DNA. In each of the systems studied, univalent ions substantially destabilize charged ligand-DNA complexes at physiological salt concentrations. This effect involves a salt dependent redistribution of counterions near the DNA. The free energy associated with the redistribution of counterions upon binding is dominated by the unfavorable change in the electrostatic ion-molecule interactions, delta delta G degrees im, rather than the change in the cratic entropy of ion organization, delta delta G degrees org. In addition, the observed slope of the salt dependence of the free energy is determined by electrostatic ion-molecule and ion-ion interactions as well as the cratic entropy of ion release. These findings are in contrast to models in which the cratic entropy of counterion release drives binding.

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

In this paper, finite-difference solutions to the nonlinear Poisson-Boltzmann (NLPB) equation are used to calculate the salt dependent contribution to the electrostatic DNA binding free energy for both the lambda cI repressor and the EcoRI endonuclease. For the protein-DNA systems studied, the NLPB method describes nonspecific univalent salt dependent effects on the binding free energy which are in excellent agreement with experimental results. In these systems, the contribution of the ion atmosphere to the binding free energy substantially destabilizes the protein-DNA complexes. The magnitude of this effect involves a macromolecular structure dependent redistribution of both cations and anions around the protein and the DNA which is dominated by long range electrostatic interactions. We find that the free energy associated with global ion redistribution upon binding is more important than changes associated with local protein-DNA interactions (ion-pairs) in determining salt effects. The NLPB model reveals how long range salt effects can play a significant role in the relative stability of protein-DNA complexes with different structures.

Elective stenting of symptomatic middle cerebral artery stenosis.

Percutaneous balloon angioplasty has been found to be useful for the treatment of intracranial atherosclerotic arterial stenosis. Nonetheless, an ongoing risk of this procedure is arterial dissection, which increases the hazards of acute closure, stroke, and restenosis. Stenting of the intracranial vasculature recently has been shown to be feasible in a variety of circumstances. To our knowledge, however, stenting of the middle cerebral artery has not been possible until now primarily because of difficulty with tracking stents across the carotid siphon. We describe the successful treatment of a symptomatic middle cerebral artery stenosis achieved using a balloon-expandable flexible coronary stent.

Emergency endovascular treatment of cerebral sinus thrombosis with a rheolytic catheter device.

Severe thrombosis of the superior sagittal, transverse, and straight sinuses developed in a 53-year-old woman. This resulted in extensive multifocal hemorrhagic venous infarction and severe intracranial hypertension refractory to intensive management. Endovascular therapy using a rheolytic catheter device in combination with a small amount of fibrinolytic agent led to rapid normalization of the intracranial pressure, allowing optimization of the cerebral perfusion pressures and was followed by steady, albeit protracted, clinical improvement. The patient not only survived but also left the hospital with minimal neurologic deficit. The rheolytic catheter endovascular treatment is, in the opinion of the authors, the treatment of choice for patients with life-threatening cerebral sinus thrombosis.

Coronary artery vasomotion after percutaneous transluminal coronary angioplasty.

Substantial evidence of postangioplasty vasoconstriction is available, both at the dilated site and distal to balloon injury, demonstrating its frequent occurrence. It is likely that even mild or moderate vasoconstriction at the site of balloon injury may create flow turbulence, promoting platelet aggregation and contributing to thrombotic vessel closure. The regulation of arterial smooth muscle tone is a complex process and should be distinguished from elastic recoil, which occurs at the site of balloon injury due to passive elastic properties of the artery, generally immediately after balloon deflation. The contribution of a variety of messengers generated by humoral, neurogenic, myogenic, and endothelium-derived factors in this regulatory process has been implicated. The possible mechanisms of post-percutaneous transluminal coronary angioplasty vasoconstriction at the dilated site (local) and in segments of coronary artery beyond the dilated site (distal) are reviewed in this article.

Upper gastrointestinal endoscopy in infants and children.

Fibreoptic endoscopy is a highly efficient diagnostic tool which is now being increasingly used in pediatric age group also. However, certain special considerations like the use of special instruments, use of general anesthesia in younger children and various indications of diagnostic and therapeutic endoscopy need to be clearly emphasized. Over a period of 24 months, 132 children underwent upper gastrointestinal endoscopic examination in our section. Diagnostic endoscopy was carried out on 102 occasions and therapeutic on 162 occasions. Most of the children below 3 years of age required general anesthesia for the procedure. Children above 3 years of age could be managed by intravenous diazepam and pentazocine. The commonest cause of upper gastrointestinal bleed in children was variceal (60.6%) followed by erosive gastritis (27.2%). In children with recurrent abdominal pain no underlying cause was detected at endoscopy. Injection sclerotherapy was found to be a safe and effective mean for control of variceal bleed and most of the foreign bodies ingested by children and still lying proximal to 2nd part of duodenum could be successfully retrieved endoscopically.

Pattern of congenital heart disease in King Fahd Specialist Hospital, Buraidah.

Three hundred and twenty (84.5%) of 379 cardiac studied in the Pediatric Cardiology Unit of King Fahd Specialist Hospital, Buraidah, between August 1988 and October 1991 had congenital heard disease. Both sexes were equally affected. Ventricular septal defects were the most common lesions (relative frequency 38.5%), followed by atrial septal defects (11.5%), pulmonary valve stenosis (9%), and patent ductus arteriosus (8%). Compared with American and European children, our patients had a paucity of obstructive aortic lesions (5% versus 109%), and an excess of atrial septal defects (11.5% versus 6.7%) and atrioventricular canal defects (5% versus 2.4%). The latter appeared to be due to the relatively high incidence of trisomy-21 in our patients, which was present in 32 (50.7%) of the 63 patients with identified etiology; that is, in 10% of the 320 patients as against a reported incidence of about 5% in other series. This comparatively high incidence was, in turn, attributable to the relatively advanced age (mean 34.0 +/- 8.3 years) of the mothers of the trisomic children. The cumulative detection rate was suboptimal: 29% at age one month, 53% at six months, and 60% at one year. There is, therefore, a need for increased awareness, especially among primary health and other front-line doctors, and earlier case detection.

Changes in adipose tissue distribution during pregnancy in overweight and obese compared with normal weight women.

OBJECTIVE: Differences in body fat distribution contribute to the metabolic abnormalities associated with overweight and obesity; however, such differences have not been adequately explored during pregnancy. Our aim was to compare longitudinal trends in maternal abdominal adipose tissue deposition during pregnancy in overweight/obese compared with normal weight women. STUDY DESIGN: Pregnant women, classified as normal weight (body mass index (BMI) <25 kg m(-2); N=61) or overweight/obese (BMI 25 kg m(-2); N=57), were enrolled in a prospective cohort study starting in the first trimester. Maternal subcutaneous (smin) and preperitoneal (pmax) fat were measured by ultrasound at five time points starting between 6 and 10 weeks gestation. The abdominal fat index (AFI), an established marker of visceral adipose tissue, was calculated as the ratio of pmax to smin. The trajectories of smin, pmax, cumulative fat index (smin plus pmax) and the AFI across pregnancy were analyzed using mixed linear models. RESULTS: The rate of maternal weight gain during pregnancy was significantly lower for overweight/obese women compared with their non-overweight counterparts (P<0.05). Accordingly, the rate of change of pmax and smin differed significantly in normal weight compared with overweight/obese women (P=0.0003 and 0.01, respectively). The cumulative fat index did not change across gestation in normal weight women, whereas it decreased for overweight/obese women (P=0.0005). The log AFI increased across pregnancy in both strata, but significantly more rapidly for normal weight compared with overweight/obese women (P=0.06). CONCLUSIONS: Adipose tissue is preferentially deposited in the more metabolically active visceral compartment as pregnancy progresses. However, this process differs in normal weight compared with overweight/obese women and may contribute to metabolic differences between these groups. Our study is a step toward a more refined description of obesity and its consequences during pregnancy.

Antioxidant and Antimicrobial Activity of Alpinia officinarum.

Alpinia officinarum is a rhizome belonging to the family zingeberaeceae. Hydro alcoholic extract by hot and cold maceration and methanol extract by percolation process Qualitative phytochemical analysis of extract of Alpinia officinarum rhizome showed a majority of the compound including tannins, alkaloids, flavonoids and saponins. Hydroalcoholic extract prepared by hot maceration process was found to contain more phenol and flavonol and it was measured as 50.1 mg/g and 54.02 mg/g, respectively. All the three extracts showed moderate to potent antimicrobial activity against the Bacillus cereus, Staphylococcus aureas, Pseudomonas auroginosa, Escherichia coli. None of the extracts showed antifungal activity against Aspergillus niger and Candida albicans. All the three extracts showed a concentration dependent radical scavenging activity by inhibiting diphenylpicrylhydrazyl free radical at the same time hydroalcoholic extract prepared by hot maceration process showed better reducing and total antioxidant activity.

Placental blood flow and the risk of preterm delivery.

The goal of this analysis was to estimate the influence of variation in uterine artery and umbilical artery resistance indices (RIs) measured across gestation on variation in the risk of preterm delivery (PTD). Analyses were carried out on data collected in a longitudinal study of 523 gravidas. Uterine and umbilical artery RIs were measured on three occasions during pregnancy (16-20 weeks gestation; 21-29 weeks gestation; and 30-36 weeks gestation). Data were analyzed using the Cox proportional hazards regression model. The primary outcome variable was birth prior to 37 weeks gestation. We found that for mothers who delivered preterm the mean uterine artery RI was consistently larger across all gestational ages, while the mean umbilical artery RI decreased significantly more slowly across gestation than for their term counterparts. In analyses pooled by type of delivery, we found that the hazard ratio (HR) for PTD was statistically significant for either uterine artery RI (HR=2.26, 95% CI: 1.65, 3.11) or umbilical artery RI (HR=3.47, 95% CI: 2.43, 4.95) after adjusting for statistically significant covariates. In stratified analyses, the hazard ratio for PTD was also positively associated with an increased uterine or umbilical artery RI in both spontaneous and indicated deliveries. Our data suggest that pregnancies with either a higher uterine or umbilical artery RI across gestation are more likely to be affected by PTD suggesting that disordered placentation resulting in compromised placental blood flow may be an important pathway to PTD.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

The electrostatic contribution to the B to Z transition of DNA.

In this paper, the finite difference nonlinear Poisson-Boltzmann (NLPB) equation is used to calculate the electrostatic contribution to the B to Z transition of DNA using detailed molecular structures of each DNA form. The electrostatic transition free energy is described as a balance between the change in intramolecular Coulombic interactions and charge-dependent interactions between the DNA and the solvent. As in many prior studies, we find that the larger electrostatic repulsions among the more closely spaced Z-DNA phosphates destabilize this form compared to B-DNA in the absence of solvent. However, as a result of the more compact three-dimensional geometry of Z-DNA, both water and salt are found to strongly stabilize this conformation to the extent that the total electrostatic free energy favors the B to Z transition in aqueous solution. Water acts not only by screening the inter-phosphate repulsions but also by solvating both charged and polar groups on Z-DNA more favorably than B-DNA. In addition, Z-DNA is stabilized by a substantially higher concentration of nearby counterions than B-DNA. The relative stabilization of Z-DNA by salt increases with increasing bulk salt concentration, leading to the high-salt B to Z transition. We find that the salt dependence of the B to Z transition free energy calculated with the NLPB equation agrees reasonably well with experimental results. Since electrostatic interactions are found to favor the Z-form, nonelectrostatic forces must be responsible for the relative stability of B-DNA in solution. An analysis of these forces suggests that the conformational entropy may play an important role.

On the role of magnesium ions in RNA stability.

Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the mental ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg(2+)-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed.

A thermodynamic framework for Mg2+ binding to RNA.

We present a model describing how Mg(2+) binds and stabilizes specific RNA structures. In this model, RNA stabilization arises from two energetically distinct modes of Mg(2+) binding: diffuse- and site-binding. Diffusely bound Mg(2+) are electrostatically attracted to the strong anionic field around the RNA and are accurately described by the Poisson-Boltzmann equation as an ensemble distributed according to the electrostatic potentials around the nucleic acid. Site-bound Mg(2+) are strongly attracted to specifically arranged electronegative ligands that desolvate the ion and the RNA binding site. Thus, site-binding is a competition between the strong coulombic attraction and the large cost of desolvating the ion and its binding pocket. By using this framework, we analyze three systems where a single site-bound Mg(2+) may be important for stability: the P5 helix and the P5b stem loop from the P4-P6 domain of the Tetrahymena thermophila group I intron and a 58-nt fragment of the Escherichia coli 23S ribosomal RNA. Diffusely bound Mg(2+) play a dominant role in stabilizing these RNA structures. These ions stabilize the folded structures, in part, by accumulating in regions of high negative electrostatic potential. These regions of Mg(2+) localization correspond to ions that are observed in the x-ray crystallographic and NMR structures of the RNA. In contrast, the contribution of site-binding to RNA stability is often quite small because of the large desolvation penalty. However, in special cases, site-binding of partially dehydrated Mg(2+) to locations with extraordinarily high electrostatic potential can also help stabilize folded RNA structures.

Physiological significance of a proximal coronary artery stenosis on a distal intramyocardial bridge: coronary flow velocity patterns pre- and post-angioplasty.

The angiographic incidence of intramyocardial bridging (MB) is 0.7-4.5% [Angelini et al.: Prog Cardiovasc Dis 25:75-88, 1983]. Morphological and physiological patterns of MB have recently been described, observing coronary flow velocity patterns, intravascular ultrasound, and angiography [Flynn et al.: Cathet Cardiovasc Diagn 32:36-39, 1994; Ge et al.: Circ Res 89:1725-1732, 1994]. We describe a reversal of the normal flow velocity characteristics within a MB, due to a hemodynamically significant stenosis in the proximal left anterior descending artery (LAD). After successful percutaneous transluminal coronary angioplasty (PTCA) of the proximal LAD stenosis, there was normalization of the flow velocity pattern within the MB and the appearance of a spike and dome pattern distal to the MB.

Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA.

A model based on the nonlinear Poisson-Boltzmann (NLPB) equation is used to study the electrostatic contribution to the binding free energy of the lambdacI repressor to its operator DNA. In particular, we use the Poisson-Boltzmann model to calculate the pKa shift of individual ionizable amino acids upon binding. We find that three residues on each monomer, Glu34, Glu83, and the amino terminus, have significant changes in their pKa and titrate between pH 4 and 9. This information is then used to calculate the pH dependence of the binding free energy. We find that the calculated pH dependence of binding accurately reproduces the available experimental data over a range of physiological pH values. The NLPB equation is then used to develop an overall picture of the electrostatics of the lambdacI repressor-operator interaction. We find that long-range Coulombic forces associated with the highly charged nucleic acid provide a strong driving force for the interaction of the protein with the DNA. These favorable electrostatic interactions are opposed, however, by unfavorable changes in the solvation of both the protein and the DNA upon binding. Specifically, the formation of a protein-DNA complex removes both charged and polar groups at the binding interface from solvent while it displaces salt from around the nucleic acid. As a result, the electrostatic contribution to the lambdacI repressor-operator interaction opposes binding by approximately 73 kcal/mol at physiological salt concentrations and neutral pH. A variety of entropic terms also oppose binding. The major force driving the binding process appears to be release of interfacial water from the protein and DNA surfaces upon complexation and, possibly, enhanced packing interactions between the protein and DNA in the interface. When the various nonelectrostatic terms are described with simple models that have been applied previously to other binding processes, a general picture of protein/DNA association emerges in which binding is driven by the nonpolar interactions, whereas specificity results from electrostatic interactions that weaken binding but are necessary components of any protein/DNA complex.

Fine-needle aspiration cytology of abdominal masses.

An investigation of the role of blind fine-needle aspiration cytology (FNAC) in the assessment of palpable abdominal masses was carried out on 196 patients: 124 hepatic, 30 retroperitoneal, and 42 other masses. All of the smears were stained either by Papanicolaou stain or by hematoxylin and eosin stain. The results of FNAC were confirmed by further investigations in all cases. FNAC correctly diagnosed 166 (84.6%) cases. Twenty (10.2%) reports were false negative, and 10 (5.1%) smears were unsatisfactory for any diagnosis. Of 124 hepatic masses, the correct diagnosis was obtained in 106 (85.4%), false-negative reports in 14 (11.2%), and unsatisfactory smears in 4 (3.2%). There were no false-positive reports. For all the lesions, the sensitivity of FNAC was 87.8%; specificity, 100%; positive predictive value, 100%; and negative predictive value, 52.4%. Five (2.5%) patients had considerable pain after the procedure.