A Secondary Analysis of Panoramic Radiographs Reveals Hotspots in the Maxillofacial Region Associated with Diabetes.

Diabetes mellitus is the putative cause of a number of pathologies occurring in the bony and soft tissues of the maxillo-facial region and is known to exacerbate other oral diseases such as periodontitis.We present the first use of clinical panoramic radiographs for a secondary analysis of disease, with a focus on identifying hotspots in the maxillofacial region that are associated with diabetes. We developed a curated data set using Consensus Landmark Points (CLPs) and used that data to develop an analysis pipeline.

Progressive cutaneous viral pigmented plaques in three Hungarian Vizslas and the response of lesions to topical tigilanol tiglate gel.

Cutaneous pigmented viral plaques is a disorder of epidermal growth caused by canine papillomavirus type 4 (CPV-4). There is currently no standard of care for managing this condition and it has not been reported in the Hungarian Vizsla. This case series documents the clinical features of canine pigmented viral plaques in Hungarian Vizsla dogs and the treatment of a severe case using a novel topical agent tigilanol tiglate (EBC-46).

Counterion condensation and shape within Poisson-Boltzmann theory.

An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes.

In vitro translation and computational analyses of human profilin multimers.

Profilin is an ubiquitous intracellular G-actin and PIP2-binding protein that is a pan-allergen. Functional native human profilin multimers have recently been described, implicating regulatory roles in cell morphology, signaling and allergies. Considering the potential importance of profilin self-association in nature, multimerization was examined using cDNAs to human profilin I (P1) and II (P2) by employing a plasmid (pCITE2a+) for in vitro transcription/radiolabeled translation.

Necessity of aromatic carboxylate anions to be planar to induce growth of cationic micelles.

It is well-known that some aromatic anions have the ability to induce viscoelastic transformation in aqueous solutions of cationic surfactants even at added salt concentrations as low as 10-20 mM. This behavior is associated with the formation of an entangled network of elongated micelles. However, the effect of aromatic ring substituents on the anion's ability to promote rapid micelle growth is not well-understood.

Calculation of the binding free energy for magnesium-RNA interactions.

The nature of the interaction between nucleic acids and divalent ions in solution is complex. It includes long-range electrostatic and short-range nonelectrostatic forces. Water molecules can be in an inner coordination shell that intervenes between the ion and its binding site.

The triplex-hairpin transition in cytosine-rich DNA.

We present a theoretical study of the self-complementary single-stranded 30-mer d(TC*TTC*C*TTTTCCTTCTC*CCGAGAAGGTTTT) (PDB ID: 1b4y) that was designed to form an intramolecular triplex by folding back twice on itself. At neutral pH the molecule exists in a duplex hairpin conformation, whereas at acidic pH the cytosines labeled by an asterisk (*) are protonated, forming Hoogsteen hydrogen bonds with guanine of a GC Watson-Crick basepair to generate a triplex. As a first step in an investigation of the energetics of the triplex-hairpin transition, we applied the Bashford-Karplus multiple site model of protonation to calculate the titration curves for the two conformations.

Induced coalescence of cations through low-temperature Poisson-Boltzmann calculations.

The computational determination of preferred binding regions of divalent counterions to nucleic acids is either inaccurate (standard Poisson-Boltzmann approaches) or extremely time-consuming (Monte Carlo or molecular dynamics simulations). A novel "selective low-temperature" Poisson-Boltzmann method is introduced that, although approximate in nature, qualitatively accounts for ion correlation and charge-transfer effects and allows for the rapid determination of such regions through an "induced coalescence" of divalent ions. The method is illustrated here for the binding of Mg(2+) to a double-helical sequence of B-form DNA (CGCGAATTCGCG) but the technique is readily applicable to locating divalent cations in other systems such as DNA-endonuclease complexes and ribozymes.

Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations.

The predictions of counterion condensation theory for divalent ions were tested by comparison with the results of Monte Carlo calculations on an all-atom model of DNA. Monovalent-divalent competition at the polyelectrolyte surface was investigated by varying the partial molar volume of divalent ions. To assess the viability of using Poisson-Boltzmann (PB) calculations for determining divalent ion concentrations at DNA surfaces, Monte Carlo (MC) calculations were compared with PB calculations using different models of the dielectric continuum.

Proton equilibria in the minor groove of DNA.

Poisson-Boltzmann calculations by Pack and co-workers suggest the presence of regions of increased hydrogen ion density in the grooves of DNA. As an experimental test of this prediction, we have attached proton-sensitive probes, with variable linker lengths, to random-sequence DNA at G sites in the minor groove. The amino groups of beta-alanine, gamma-aminobutyric acid (GABA), and epsilon-aminocaproic acid have been coupled at pH 5, via a formaldehyde link, to the exocyclic amino group of guanine, utilizing a reaction that has been extensively investigated by Hanlon and co-workers.

Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA.

The counterion density and the condensation region around DNA have been examined as functions of both ion size and added-salt concentration using Metropolis Monte Carlo (MC) and Poisson-Boltzmann (PB) methods. Two different definitions of the "bound" and "free" components of the electrolyte ion atmosphere were used to compare these approaches. First, calculation of the ion density in different spatial regions around the polyelectrolyte molecule indicates, in agreement with previous work, that the PB equation does not predict an invariance of the surface concentration of counterions as electrolyte is added to the system.

The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems.

The results of variable dielectric coefficient Poisson-Boltzmann calculations of the counter-ion concentration in the vicinity of an all-atom model of the B-form of DNA are presented with an emphasis on the importance of spatial variations in the dielectric properties of the solvent, particularly at the macro-ion-solvent interface. Calculations of the distribution of hard-sphere electrolyte ions of various dimensions are reported. The presence of a dielectric boundary significantly increases the magnitude of the electrostatic potential with a concomitant increase in the accumulation of small counter-ions in the groove regions of DNA.

Acidic domains around nucleic acids.

The hydrogen ion concentration in the vicinity of DNA was mapped out within the Poisson-Boltzmann approximation. Experimental conditions were modeled by assuming Na-DNA to be solvated in a buffer solution containing 45 mM Tris and 3 mM Mg cations at pH 7.5.

Counterion distribution around DNA: variation with conformation and sequence.

The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions.

The molecular structure and charge distribution of phorbol: parent compound of the tumor promoting phorbol diesters.

The geometry of phorbol, parent compound of the very highly active tumor promoting phorbol diesters, was totally optimized starting from the crystal structure of phorbol-5-bromofuroate-chloroform solvate (Petterson et al., J. Chem.

Quantum chemical calculations on the two-step mechanism of proflavin binding to DNA.

Quantum chemical calculations on the binding of proflavin to DNA lead to a model in which the outside binding to a phosphate group leads to an induced fit in the intercalation receptor site. The calculations suggest hydrogen bonding of the amine groups of the outside bound proflavin to the anionic oxygen of the backbone phosphate. The resulting partial neutralization facilitates the conformational transitions required for intercalation.

Quantum chemical studies of the metabolism of polycyclic aromatic amines and the stabilities and electrophilicities of their arylnitrenium ions in relation to their mutagenic/carcinogenic potencies.

Electronic parameters related to the cytochrome P450-catalyzed reactions of eight polycyclic aromatic amines have been calculated using all valence electron semiempirical molecular orbital methods. The reactions considered lead to the presumably carcinogenic arylnitrenium ions and to the competing hydroxylation and epoxidation products. The stabilities of the arylnitrenium ions relative to the N-hydroxylamines and their sulfate esters were also calculated, together with electrophilic reactivity parameters of the ions.

Origins of the specificity in the intercalation of ethidium into nucleic acids. A theoretical analysis.

The sequence preferences observed in the intercalative binding of ethidium to dinucleoside phosphates have been theoretically examined. This specificity is for pyrimidine (3'--5') purine sequences as compared to their purine (3'--5') pyrimidine sequence isomers. It is shown that the stacking energies between the ethidium cation and the base pairs are fairly constant for all combinations of bases at the intercalation site.

Kinked DNA. Energetics and conditions favoring its formation.

Theoretical calculations demonstrate that the formation of kinks in DNA in the manner proposed by Crick and Klug produces a conformation which corresponds to a local energy minimum when the phosphate backbone is charged. This conformation becomes the global minimum under certain conditions which neutralize the anionic backbone oxygens. A sequence preference for kink formation is predicted.