Draft Genome Sequences of 9 Actinobacteria from the Family Microbacteriaceae Associated with Insect- and Nematode-Damaged Plants.

Draft genome sequences of 9 strains of known and putative new species of Microbacteriaceae isolated from insect- and nematode-damaged plants were generated using Illumina technology. The data obtained will contribute to the development of the genome-based prokaryote taxonomy and the knowledge on the biology of the microbial group investigated.

Diagnostic of laser-induced plasma using Abel inversion and radiation modeling.

A method based on matching synthetic and experimental emissivity spectra was applied to spatially resolved measurements of a laser-induced plasma ignited in argon at atmospheric pressure. The experimental emissivity spectra were obtained by Abel inversion of intensity spectra measured from a thin plasma slice perpendicular to the plasma axis. The synthetic spectra were iteratively calculated from an equilibrium model of plasma radiation that included free-free, free-bound, and bound-bound transitions. From both the experimental and synthetic emissivity spectra, spatial and temporal distributions of plasma temperature and number densities of plasma species (atoms, ions, and electrons) were obtained and compared. For the best-fit synthetic spectra, the temperature and number densities were read directly from the model; for experimental spectra, these parameters were obtained by traditional Boltzmann plot and Stark broadening methods. In both cases, the same spectroscopic data were used. Two approaches revealed a close agreement in electron number densities, but differences in plasma excitation temperatures and atom number densities. The trueness of the two methods was tested by the direct Abel transform that reconstructed the original intensity spectra for comparing them to the measured spectra. The comparison yielded a 9 and 13% difference between the reconstructed and experimental spectra for the numerical and traditional methods, respectively. It was thus demonstrated that the spectral fit method is capable of providing more accurate plasma diagnostics than the Boltzmann plot and Stark broadening methods.

Spectroscopic identification of reactive porphyrin motions.

Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, (57)Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.

Molecular orientation of asphaltenes and PAH model compounds in Langmuir-Blodgett films using sum frequency generation spectroscopy.

Asphaltenes are an important class of compounds in crude oil whose surface activity is important for establishing reservoir rock wettability which impacts reservoir drainage. While many phenomenological interfacial studies with crude oils and asphaltenes have been reported, there is very little known about the molecular level interactions between asphaltenes and mineral surfaces. In this study, we analyze Langmuir-Blodgett films of asphaltenes and related model compounds with sum frequency generation (SFG) vibrational spectroscopy. In SFG, the polarization of the input (vis, IR) and output (SFG) beams can be varied, which allows the orientation of different functional groups at the interface to be determined. SFG clearly indicates that asphaltene polycyclic aromatic hydrocarbons (PAHs) are highly oriented in the plane of the interface and that the peripheral alkanes are transverse to the interface. In contrast, model compounds with oxygen functionality have PAHs oriented transverse to the interface. Computational quantum chemistry is used to support corresponding band assignments, enabling robust determination of functional group orientations.