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At least 307 records · Page 17Linked to original sources
PubMed1996

Infrared emission spectra of candidate interstellar aromatic molecules.

Interstellar dust is responsible, through surface reactions, for the creation of molecular hydrogen, the main component of the interstellar clouds in which new stars form. Intermediate between small, gas-phase molecules and dust are the polycyclic aromatic hydrocarbons (PAHs). Such molecules could account for 2-30% of the carbon in the Galaxy, and may provide nucleation sites for the formation of carbonaceous dust. Although PAHs have been proposed as the sources of the unidentified infrared emission bands that are observed in the spectra of a variety of interstellar sources, the emission characteristics of such molecules are still poorly understood. Here we report laboratory emission spectra of several representative PAHs, obtained in conditions approximating those of the interstellar medium, and measured over the entire spectral region spanned by the unidentified infrared bands. We find that neutral PAHs of small and moderate size can at best make only a minor contribution to these emission bands. Cations of these molecules, as well as much larger PAHs and their cations, remain viable candidates for the sources of these bands.

Extraterrestrial Environment↗
PubMed1988

How climate evolved on the terrestrial planets.

Planets with temperate, earthlike climates were once thought to be rare in our galaxy. Mathematical models now suggest that if planets do exist outside the solar system, many of them might be habitable.

Astronomical Phenomena↗
PubMed1991

End of the Proterozoic eon.

Living organisms have inhabited the surface of our planet for nearly four billion years. Yet the plants and animals that define our everyday existence have far more recent origins. The ancestors of modern trees and terrestrial animals first colonized land only about 450 million years ago. In the oceans, animals have a longer record, but macroscopic invertebrates did not appear even there until about 580 million years ago--roughly 85 percent of the way through life's history. The earliest animals, which are collectively referred to as the Ediacaran fauna (after the Ediacara Hills in southern Australia), have intrigued paleontologists since their discovery more than 50 years ago [see "The Emergence of Animals," by Mark A. S. McMenamin; Scientific American, April 1987]. The surprisingly young age of the fossils presents a most interesting puzzle. If life is so ancient, why did animals appear so late in the evolutionary day? Why--once the basic blueprint of life was drawn--did animals not emerge for more than three billion years? Alternatively, is the fossil record misleading? Is it possible that animals are far older than the record suggests?

Animals↗
PubMed1988

Intermolecular potential for thermal H2O-He collisions.

Theoretical potentials for rotational excitation of H2O by He were constructed via several methods, all of which start with a large basis set SCF interaction. The semiempirical Hartree-Fock with damped dispersion (HFD) model adds a damped long-range attraction with parameters adjusted to fit experimental total differential cross sections. Purely ab initio potentials add correlation energies obtained via perturbation theory (MP2 and MP4) or a variational method (ICF1). Scattering calculations were performed on all surfaces to compare with available beam scattering and pressure broadening data and to assess sensitivity of state-to-state rates to uncertainties in the potential. From comparison with the limited experimental data, the ICF1 surface appears to be marginally better than the MP4 surface. Thermal rates calculated from this surface should be accurate to better than 50%, at least for the larger, more important rates.

Chemical Phenomena↗
PubMed1991

Calculations of H2O microwave line broadening in collisions with He atoms: sensitivity to potential energy surfaces.

Broadening parameters for three microwave lines of water at 22.2, 183.3, and 380.2 GHz, in a bath of helium atoms, are calculated using accurate molecular scattering S matrices obtained from two theoretical potentials presented by Palma et al., J. Chem. Phys. 89, 1401 (1988). For the 22 GHz line results are in substantial agreement with values presented in that work, indicating the accuracy of approximate methods used there. The present work improves the potential energy surfaces, computed from perturbation theory (MP4) and variational interacting correlated fragments (ICF1) wave functions, by correcting them for basis set superposition error (BSSE), and recomputes the line broadening using a different procedure for fitting computed energy points. In addition, the entire set of calculations are repeated with a quite different basis set for orbital expansion to establish the reliability of the potential energy surface. We show that adjustments for superposition error are essential, and that broadening cross sections computed from the new surfaces are changed 10%-30% from the old, significantly improving agreement with experiment. The MP4 BSSE adjusted surface appears to be the most accurate, giving room temperature broadenings of 8.9, 11.8, and 10.0 angstroms2 compared with experimental determinations of 12.2 +/- 1.2, 11.9, and 11.2 angstroms2 for the 22, 183, and 380 GHz lines, respectively. Thus, computed line to line variation is larger than observed. The ICF1 BSSE adjusted results for pressure broadening cross section parallel those from the MP4 BSSE calculations but are about 10% smaller. We believe our computed results are stable with respect to basis set for orbital expansion and that the scattering calculations are accurate. Any theoretical inadequacy has been pinpointed to too few points on the potential energy surface resulting in an inadequate description of the angle dependence. It is not clear whether the present discrepancy between computation and experiment stems from this or from errors in the experimental values, although we show some indication that additional information on the surface might decrease the computed broadenings, worsening agreement with experiment.

Computer Simulation↗
PubMed1991

Calculations on the rate of the ion-molecule reaction between NH3+ and H2.

The rate coefficient for the ion-molecule reaction NH3(+) + H2 --> NH4(+) + H has been calculated as a function of temperature with the use of the statistical phase space approach. The potential surface and reaction complex and transition state parameters used in the calculation have been taken from ab initio quantum chemical calculations. The calculated rate coefficient has been found to mimic the unusual temperature dependence measured in the laboratory, in which the rate coefficient decreases with decreasing temperature until 50-100 K and then increases at still lower temperatures. Quantitative agreement between experimental and theoretical rate coefficients is satisfactory given the uncertainties in the ab initio results and in the dynamics calculations. The rate coefficient for the unusual three-body process NH3(+) + H2 + He --> NH4(+) + H + He has also been calculated as a function of temperature and the result found to agree well with a previous laboratory determination.

Ammonia↗
PubMed1993

Infrared laser spectroscopy of jet-cooled carbon clusters: the bending dynamics of linear C9.

We report improved measurements for the nu 6 antisymmetric stretch fundamental and observation of the (nu 6 + nu 15)-nu 15 and (nu 6 + 2 nu 15)-2 nu 15 hot bands of the linear C9 carbon cluster by direct absorption diode laser spectroscopy of a supersonic carbon cluster beam. Analysis of these bands characterizes C9 as a semirigid molecule with a bending potential similar to that of C5 and further evidences the alternation in degree of rigidity of linear carbon clusters with the g-u symmetry of the HOMO.

Astronomical Phenomena↗
PubMed1991

Two-dimensional life?

A model [Wächtershäuser, G. (1988) Microbiol. Rev. 52, 452-484], according to which life started in the form of a monomolecular layer of interacting anionic metabolites electrostatically bound to a positively charged surface, is examined critically. The model raises a number of thermodynamic and kinetic difficulties.

Animals↗
PubMed1992

On the nature of global classification.

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

Biological Evolution↗
PubMed1993

Composite, large spirochetes from microbial mats: spirochete structure review.

Phenomena previously unknown in free-living spirochetes are reported: large-sized cells with variable diameter (length to 100 microns, width between 0.4 and 3.0 microns), composite structure (smaller spirochetes inside larger ones), and positive phototropic behavior. These bacteria, Spirosymplokos, are compared with all other spirochete genera. The large spirochete, grown in mixed culture, was studied live and by transmission EM. The protoplasmic cylinder was replete with spherical granules 20-32 nm in diameter, and three to six periplasmic 26-nm flagella were inserted subterminally. Comparably granulated and flagellated small spirochetes were located inside the protoplasmic cylinder and in the periplasm of the large ones. When exposed to air, movement became erratic, protoplasmic cylinders retracted to lie folded inside the outer membrane, and refractile membranous structures formed. From one to four structures per still-moving spirochete were seen. Spirosymplokos was enriched from laboratory samples exposed to oxygen-rich and desiccating, but not dry, conditions for at least 4 mo after removal of microbial mat from the field.

Microscopy, Electron↗
PubMed1993

In vitro selection of optimal DNA substrates for T4 RNA ligase.

We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 RNA ligase. We find that the ensemble of selected sequences ligated about 10 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly, the majority of the selected sequences approximated a well-defined consensus sequence.

Bacteriophage T4↗
PubMed1993

An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum.

The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by the polymerase chain reaction, and the resulting products were sequenced directly. The two organisms are closely related by this measure (over 98% similar). However, they differ in that the (lone) 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not seen in the corresponding gene of Pyrobaculum islandicum. To our knowledge, this is the only intron so far reported in the small subunit rRNA gene of a prokaryote. Upon excision the intron is circularized. A secondary structure model of the intron-containing rRNA suggests a splicing mechanism of the same type as that invoked for the tRNA introns of the Archaea and Eucarya and 23S rRNAs of the Archaea. The intron contains an open reading frame whose protein translation shows no certain homology with any known protein sequence.

Amino Acid Sequence↗
PubMed1993

Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane.

A 16-residue peptide [(Ala-Glu-Ala-Glu-Ala-Lys-Ala-Lys)2] has a characteristic beta-sheet circular dichroism spectrum in water. Upon the addition of salt, the peptide spontaneously assembles to form a macroscopic membrane. The membrane does not dissolve in heat or in acidic or alkaline solutions, nor does it dissolve upon addition of guanidine hydrochloride, SDS/urea, or a variety of proteolytic enzymes. Scanning EM reveals a network of interwoven filaments approximately 10-20 nm in diameter. An important component of the stability is probably due to formation of complementary ionic bonds between glutamic and lysine side chains. This phenomenon may be a model for studying the insoluble peptides found in certain neurological disorders. It may also have implications for biomaterials and origin-of-life research.

Amino Acid Sequence↗
PubMed1993

Z-DNA binding protein from chicken blood nuclei.

A protein (Z alpha) that appears to be highly specific for the left-handed Z-DNA conformer has been identified in chicken blood nuclear extracts. Z alpha activity is measured in a band-shift assay by using a radioactive probe consisting of a (dC-dG)35 oligomer that has 50% of the deoxycytosines replaced with 5-bromodeoxycytosine. In the presence of 10 mM Mg2+, the probe converts to the Z-DNA conformation and is bound by Z alpha. The binding of Z alpha to the radioactive probe is specifically blocked by competition with linear poly(dC-dG) stabilized in the Z-DNA form by chemical bromination but not by B-form poly(dC-dG) or boiled salmon-sperm DNA. In addition, the binding activity of Z alpha is competitively blocked by supercoiled plasmids containing a Z-DNA insert but not by either the linearized plasmid or by an equivalent amount of the parental supercoiled plasmid without the Z-DNA-forming insert. Z alpha can be crosslinked to the 32P-labeled brominated probe with UV light, allowing us to estimate that the minimal molecular mass of Z alpha is 39 kDa.

Animals↗
PubMed1996

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life.

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. "Kingdoms" and "Domains" are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae.

Animals↗
PubMed1990

Diffuse reflection from a stochastically bounded, semi-infinite medium.

In order to determine the diffuse reflection from a medium bounded by a rough surface, we consider the problem of radiative transfer in a boundary layer characterized by a statistical distribution of heights. For the case that the surface is defined by a multivariate normal probability density, we derive the propagation probability for rays traversing the boundary layer and, from that probability, a corresponding radiative transfer equation. A solution of the Eddington (two stream) type is found explicitly, and examples are given. The results should be applicable to reflection from the regoliths of solar system bodies, as well as from a rough ocean surface.

Astronomical Phenomena↗
PubMed1989

Distribution of inorganic species in two Antarctic cryptoendolithic microbial communities.

Chemical differences were noted between two Antarctic cryptoendolithic (hidden within rock) microenvironments colonized by different microbial communities. Microenvironments dominated by cyanobacteria (BPC) had a higher pH (pH 7-8) than those dominated by lichen (LTL) (pH 4.5-5.5). In order to understand the interactions between the microbiota and the inorganic environment, the inorganic environment was characterized. Water-soluble, carbonate-bound, metal-oxide, organically bound, and residual inorganic species were sequentially extracted from rock samples by chemical means. Each fraction was then quantified using inductively coupled plasma atomic emission spectrometry. BPC contained much more water-soluble and carbonate-bound Ca and Mg than LTL. Metal-oxide species of Al, Fe, and Mn were more abundant in LTL than BPC. Metal oxides appeared to be mobilized (in the order Mn > Fe > Al) from the LTL lichen zone but remained immobile in BPC sandstone. The distribution of K and P bound to metal oxide reflected the distribution of iron oxide in LTL, an indication of the importance of iron in controlling the availability of nutrients in this ecosystem. Metal oxides in turn were likely controlled or influenced by organic matter associated with the lichen community. Despite overall depletion of Fe, Al, and K in the lichen zone, SEM X-ray analysis showed that they were enriched in fungal hyphae. Water-soluble P was present despite the presence of metal oxides, which sequester phosphate. This has biological relevance since P is an essential nutrient.

Antarctic Regions↗
PubMed1993

Modeling study on the cleavage step of the self-splicing reaction in group I introns.

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

Animals↗