Cosmic dust and our origins

The small solid particles in the space between the stars provide the surfaces for the production of many simple and complex molecules. Processes involving the effects of ultraviolet irradiation of the thin (hundredth micron) mantles are shown to produce a wide range of molecules and ions also seen in comets. Some of the more complex ones inferred from laboratory experiments are expected to play an important role in the origin of life. An outline of the chemical evolution of interstellar dust as observed and as studied in the laboratory is presented. Observations of comets are shown to provide substantial evidence for their being fluffy aggregates of interstellar dust as it was in the protosolar nebula, i.e. the interstellar cloud which collapsed to form the solar system. The theory that comets may have brought the progenitors of life to the earth is summarized.     

The Computational Chemistry Prototyping Environment

Evolving technologies, as exemplified by computational grids and Web services, have made it possible to solve new scientific problems that would not have been feasible previously. In order to make such advances available to the community in general and to be able to solve new problems, not necessarily from the same discipline, it is imperative to build tools that provide a common user interface in order that application programmers and users do not have to be concerned with particulars of Web services and their underlying code, computational platforms, or with data file formats. We will describe our efforts in creating a computational chemistry environment that encompasses a general scientific workflow environment, a domain specific example for quantum chemistry, our ongoing design of a workflow user interface, and our efforts at database integration.     

Book Reviews

Unsigned book reviews are by the Book Review Editor.     

Prevalence of voice disorders in African American and European American preschoolers

Several studies have reported prevalence rates for voice disorders in school-aged children. Less is known, however, about such prevalence in preschoolers, and whether racial, ethnic, or cultural diversity may influence it. The presence of voice disorders in a total of 2445 African-American and European-American preschool children, 1246 males and 1199 females, from 2 to 6 years of age is reported here. Presence of a voice disorder characterized by hoarseness was identified by a three-prong approach including teacher identification, investigator screening, and parent identification. Speech-language pathologists listened individually to each child's speech as they engaged each child in play-conversation activities. A voice disorder was identified on the basis of the judgment of two speech-language pathologists. Voice disorders characterized by hoarseness were identified in 95 children or 3.9% of the total sample by the investigators. Statistical analysis revealed no significant differences for age, gender, or race.     

A two-stage nonlinear cochlear model possesses automatic gain control

A model of the cochlea is explored using as stimuli two simultaneously presented sinusoids of equal amplitude. The model consists of two stages: a linear bandpass filter, followed by a reservoir-type representation of the hair-cell/nerve-fiber complex. Fast Fourier transforms of the model's output were computed. While the amplitudes of the individual response components were strongly nonlinear functions of intensity, the ratio of the magnitudes of the response components at the frequencies of the two stimulating sinusoids was found to be nearly equal, over a wide intensity range, to the ratio of the amplitudes which those stimulating sinusoids possessed at the output of the filter. Thus the reservoir stage exerts "automatic gain control".     

Neuronal activation by GPI-linked neuroligin-1 displayed in synthetic lipid bilayer membranes

We have characterized, in vitro, interactions between hippocampal neuronal cells and silica microbeads coated with synthetic, fluid, lipid bilayer membranes containing the glycosylphosphatidyl inositol (GPI)-linked extracellular domain of the postsynaptic membrane protein neuroligin-1. These bilayer-neuroligin-1 beads activated neuronal cells to form presynaptic nerve terminals at the point of contact in a manner similar to that observed for live PC12 cells, ectopically expressing the full length neuroligin-1. The synthetic membranes exhibited biological activity at neuroligin-1 densities of approximately 1 to 6 proteins/microm(2). Polyolycarbonate beads with neuroligin-1 covalently attached to the surface failed to activate neurons despite the fact that neuroligin-1 binding activity is preserved. This implies that a lipid membrane environment is likely to be essential for neuroligin-1 activity. This technique allows the study of isolated proteins in an environment that has physical properties resembling those of a cell surface; proteins can diffuse freely within the membrane, retain their in vivo orientations, and are in a nondenatured state. In addition, the synthetic membrane environment affords control over both lipid and protein composition. This technology is easily implemented and can be applied to a wide variety of cellular studies.     

Facile purification of rare cucurbiturils by affinity chromatography

A practical method for the separation and purification of cucurbituril (CB) hexamers was developed on the basis of affinity chromatography using aminopentylaminomethylated polystyrene beads. This recyclable resin, which can be used repeatedly, facilitates the general preparation of cucurbituril derivatives and compensates for the usually moderate yields and mixed products that characterize the acid-catalyzed synthesis of CB derivatives. This technique allows convenient, rapid isolation of rare substituted cucurbiturils, including hexacyclohexanocucurbit[6]uril and dodecamethylcucurbit[6]uril. [reaction: see text]     

Relative energies of substituted benzene valence isomers

Ab initio calculations employing the STO-3G basis set are used to obtain the relative energies of the benzene valence isomers and some selected monosubstituted derivatives. We find that 3,3'-bicyclopropenyl, the least stable of the five (CH)₆ examined, is slightly more stable in the anti conformation than the gauche (Φ = 45°) conformation in agreement with experiment. Substituents are calculated to produce significant changes in the relative energies of the benzene valence isomers. The ground-state isomerization of 1-Dewar benzeneearbinyl cation to benzyl cation is more exothermic than the aromatization of Dewar benzene, but is, in contrast to the latter, symmetry-allowed.     

Preparation and analysis of oligonucleotides containing the c4'-oxidized abasic site and related mechanistic probes

The C4'-oxidized abasic site (C4-AP) is produced by a variety of DNA damaging agents. This alkali labile lesion can exist in up to four diastereomeric cyclic forms, in addition to the acyclic keto-aldehyde. Synthetic oligonucleotides containing the lesion were prepared from a stable photochemical precursor. Chemical integrity of the lesion containing oligonucleotides was probed using phosphodiesterase lability. Analysis of the 3',5'-phosphate diester of the monomeric lesion released from single diastereomers of photolabile precursors by 1H NMR indicates that isomerization of the hemiacetal and/or hemiketal is rapid. The syntheses and characterization of oligonucleotides containing configurationally stable analogues of C4-AP, which serve as mechanistic probes for deciphering the structural basis of the biochemical and biological effects of the C4'-oxidized abasic lesion, are also described.