Identification of single stranded regions of DNA by enzymatic digestion with matrix-assisted laser desorption/ionization analysis

Elucidating structure function relationships of DNA in cellular processes requires fast, reliable methods that can be applied to picomole amounts of sample. Higher order structure can be inferred by distinguishing paired and unpaired regions. It is shown here that enzymatic digestion coupled with product analysis by matrix-assisted laser desorption ionization (MALDI) is able to identify unpaired bases within structured DNA regions. The method is demonstrated with DNA duplexes having a five nucleotide mismatch as a 5' overhang, a 3' overhang, and an internal loop. Exo- and endonuclease digestions are performed under solution conditions (temperature, annealing, and enzyme buffers) which promote base pairing and specific enzyme activity. For each type of mismatch, the length and sequence of the single stranded region can be inferred from MALDI spectra taken as a function of digestion time.     

A Hilbert-Vlasov code for the study of high-frequency plasmabeatwave accelerator

High-frequency beatwave simulations relevant to the University of California at Los Angeles (UCLA) experiment with relativistic eulerian hybrid Vlasov code are presented. These Hilbert-Masov simulations revealed a rich variety of phenomena associated with the fast particle dynamics induced by beatwave experiment for a high ratio of driver frequency to plasma frequency ω_pump/ω_plasma ≈33. The present model allows us to extend detailed modeling to frequency ratios greater than the current practical maximum of 10 or so, for Vlasov or particle-in-cell (PIC) codes, by replacing the Maxwell equations by mode equations for the electromagnetic Vlasov code. Numerical results, including beat frequency chirping (i.e., pump frequency linearly decreasing with time), show that the amplitude limit due to relativistic detuning can be enhanced with accelerated particles up to the ultrarelativistic energies with a high-acceleration gradient of more than 25 GeV/m     

Quantitative analysis of the mono- and sesquiterpenoids of douglas-fir sapwood by solvent extraction and gas chromatography with mass selective detection

In order to investigate the relationship between terpenoid content and black bear foraging preference, an analytical method was required to quantify mono- and sesquiterpenoids present in Douglas-fir sapwood. Sapwood samples were scraped from trees, immediately frozen in liquid nitrogen, and then homogenized. A simple extraction requiring no clean-up step was performed with ethyl acetate. Extracts were analyzed by gas chromatography with mass selective detection versus external standards. The recoveries of 22 terpenoids from fortified controls were approximately 90% with good precision (relative standard deviations of approximately 10%).     

Decomposition of regular subsemigroup lattices

Communicated by Norman R. Reilly     

Effect of an inhibitor on high-speed turbulent flames and the transition to detonation

The influence of an inhibitor (CF₃Br or Halon 1301) on the propagation of high-speed turbulent flames, quasi-detonations and the transition to detonation has been investigated for methane-air, propane-air and acetylene-air mixtures. The experiments are carried out in a 13 m tube (15 cm diameter) filled with regularly spaced orifice plates (blockage ratio of 0.39) to ensure rapid flame acceleration. In all cases, the addition of the inhibitor reduces the turbulent flame velocity and extinguishes the flame with sufficient inhibitor concentration (2.7% and 7.5% for methane-air and propane-air, respectively). For acetylene-air mixtures, the quasi-detonation speed is progressively reduced with increasing inhibitor concentration and eventually causes the failure of the quasi-detonation and transition back to a fast turbulent flame. The inhibitor also narrows the propagation limits in all cases. To elucidate the inhibition mechanism, detailed modelling of both the turbulent flame structure as well as the chemical kinetics are required.     

Energy Landscape Exploration of Sub‐Nanometre Copper–Silver Clusters

The energy landscapes of sub‐nanometre bimetallic coinage metal clusters are explored with the Threshold Algorithm coupled with the Birmingham Cluster Genetic Algorithm. Global and energetically low‐lying minima along with their permutational isomers are located for the Cu${_4 }$ Ag${_4 }$ cluster with the Gupta potential and density functional theory (DFT). Statistical tools are employed to map the connectivity of the energy landscape and the growth of structural basins, while the thermodynamics of interconversion are probed, based on probability flows between minima. Asymmetric statistical weights are found for pathways across dividing states between stable geometries, while basin volumes are observed to grow independently of the depth of the minimum. The DFT landscape is found to exhibit significantly more frustration than that of the Gupta potential, including several open, pseudo‐planar geometries which are energetically competitive with the global minimum. The differences in local minima and their transition barriers between the two levels of theory indicate the importance of explicit electronic structure for even simple, closed shell clusters.     

Biosynthetic insights provided by unusual sesterterpenes from the medicinal herb Aletris farinosa

A series of novel sesterterpenes (2–6) have been isolated from the roots of Aletris farinosa and structurally characterized by MS, NMR, and X-ray crystallography in conjunction with computational modeling. Their structures provide new insights into the mechanisms of sesterterpene biosynthesis. Specifically, we propose with support from density functional theory computations that the configuration at a single stereocenter determines the fate of a key tetracyclic carbocationic intermediate, derived from an oxidogeranylfarnesol precursor. Whereas one epimer of the carbocation undergoes H⁺ elimination to give 6, the other undergoes a spectacular cascade of seven 1,2-methyl and hydride migrations leading to the previously unreported carbon skeleton of 5. Theoretical calculations suggest that the cascade is triggered by substrate preorganization in the enzyme active site.     

Well‐Defined Palladium Nanoparticles Supported on Siliceous Mesocellular Foam as Heterogeneous Catalysts for the Oxidation of Water

Herein, we describe the use of Pd nanoparticles immobilized on an amino‐functionalized siliceous mesocellular foam for the catalytic oxidation of H₂O. The Pd nanocatalyst proved to be capable of mediating the four‐electron oxidation of H₂O to O₂, both chemically and photochemically. The Pd nanocatalyst is easy to prepare and shows high chemical stability, low leaching, and recyclability. Together with its promising catalytic activity, these features make the Pd nanocatalyst of potential interest for future sustainable solar‐fuel production.